A Picspam Recap of Mass Effect (Part 2)
Mar. 19th, 2012 04:44 pmBack to Part One (in which the Normandy has a perfectly ordinary shakedown cruise, creepy nightmare visions are had, and hey, killer robot zombies, those are always fun)
Okay, things are getting a little tangled right now, so feel free to go back to those handy bullet points in the first post. We've visited the Artermis Tau cluster and found Liara, so that's one out of three completed. Enough with these subplots; on to the next plot world! To Noveria! It's a corporate-owned planet, and a blizzard is raging as our heroes arrive.
There's a bit of a misunderstanding over weapons and who gets to carry them, but eventually Shepard manages to get to the heart of this particular plot world: Matriarch Benezia is here. Right now. With, apparently, a mysterious cargo and a bunch of commandos in tow. Unfortunately, she went up to a research station that's been made inaccessible by air due to the storm, and getting a garage pass to use ground transport is a bit of a hassle that involves taking down the corrupt administrator of the place, winning a firefight in an office, exposing dirty cops, and saving two people's careers.

Again, this is why nobody ever asks Shepard to do normal things, like picking up some milk at the store. "Oh, and on the way, I ran into this supervillain who's been using the milk to build a nuclear weapon, so I stopped him and rescued the twelve puppies he'd kept trapped in his basement. You wanted 2%, right?"
Shepard finally gets to the garage... and she's promptly attacked by geth. After taking them out, our heroes realize they must've been smuggled in via Benezia's cargo containers. Sneaky. And off we go, to the Peak 15 research station!

This is the best part of the Mako: if you're in a hurry, you can totally just drive over everything in your path. MAKO SMASH.
Upon reaching the station, Shepard and company run into some creepy bug things that instantly attack. Apparently, they're rachni. Whaaaaaat. The rachni, remember, are the ultra-agressive race the krogan fought to extinction a thousand years back. Not "nearly to extinction". These guys were gone-zo. So it's understandably baffling to have them suddenly trying to chew off your face.

Ouch. Has... has anyone tried telling them they're not supposed to exist? That might work.
There's another digression while our heroes try to get the research station operational again (it's in "holy-crap-panic" mode, with everything shut down), which includes the line:
Virtual Assistant: It looks like you're trying to restore this facility. Would you like help?
So, yeah, Clippy still exists in the future.
Anyway. Our heroes fight their way through the rachni, argue with computers for a while, and eventually get everything up and running again, which lets them take a tram to where a bunch of scientists and security personnel are holed up. After a great deal of waffling about nondisclosure agreements, the scientists admit that they've been running experiments on a rachni egg that was discovered in cryo-suspension aboard a ship - the egg hatched unexpectedly (it was a thousand years old, after all), and turned out to contain a rachni queen. She was used to breed weaponized "soldiers" - mindless killing machines - for use as weapons. Aaand this all came back to bite everyone in the ass when the mindless killing machines got loose and started, er, mindlessly killing.
While investigating all this, Shepard more-or-less accidentally manages to cure a plague and expose a sleeper agent for Benezia. As you do. Eventually, our heroes find Benezia and confront her, which is an awkward family reunion for Liara, since her mom immediately starts trying to kill her.

Mostly I just like the dramatic lighting in this shot.
Conveniently, after all her associates are dead, Benezia has a jolt of self-awareness and seems to come back to herself. She talks a bit about Saren's really creepy giant gloved lightning hand starship, which apparently the geth didn't build - she doesn't know where it came from. But the longer you stay on the ship, the more awesome Saren seems, and the more you want to hang out with him and, you know, kill people for him and stuff. Benezia has managed to seal part of her mind away from this indoctrination, temporarily, which is how she's able to communicate now.
She reveals that Saren is looking for the Mu Relay, which apparently is what'll lead him to that all-important Conduit, whatever it is - this relay been lost for millennia, but the rachni have this cross-generational memory thing going, and so Benezia was sent to get the information from the rachni queen. She sent the coordinates to Saren already, but manages to give a copy to Shep. But that's only part of the story - without knowing Saren's final destination, the location of the relay itself is useless (it's like knowing the location of an airport, rather than the final destination). But it's better than wandering aimlessly and taking on random subplots.
But Benezia loses control again, and Shep is forced to kill her before she can kill them. Poor Liara is pretty traumatized by the whole thing. This game really likes breaking its characters.

Also, her mom's last words are "No light? They always said there would be a-", which is not exactly reassuring.
After Benezia dies, Shepard goes over to check out the rachni queen, and... one of Benezia's dead associates goes all possessed-zombie and staggers over to say hi.

Braaaaains... I mean, 'sup?
Turns out that's the only way the rachni queen can communicate, and she still communicates in a very confusing/poetic way. "This one serves as our voice. We cannot sing. Not in these low spaces. She has colours we have no name for." Think of them as the, uh, zombie-possessing beat poets of the Mass Effect universe. *snap snap*
Anyway, the rachni queen eventually manages to get across that she doesn't really know what the heck happened with the whole rachni war thing since she was just an egg at the time, and that in this instance, her children have essentially been kept away from her and have been programmed to be mindless killing machines and need to be destroyed. All in all, she seems like a pretty decent giant bug alien, so Shepard, with a sneaking suspicion that this is gonna come back to bite her in the ass in some later game, decides to let her go. (This, by the way, is one of the major Paragon decisions of the game - the Renegade option is to kill the rachni queen.)
Back to the Normandy, to report to the Council, who are understandably a little vexed that Shepard has let the rachni queen go, given how the rachni almost took over the galaxy that one time. Juuust a little vexed. Since this is pretty much the Council's default reaction to Shepard, she's largely unfazed.
Time for another crew conversation? I think so! Shepard does some more serious flirting with Kaidan, and there's an awkward conversation where Kaidan's all "Uh, but I thought you and Liara were-". But nope, this is a Shepard/Kaidan playthrough, so they do some more flirting. They really are kind of adorable.

D'awww.
Kaidan reveals a seriously bad bit of his past, at the school for biotics he attended - one of his instructors snapped and started hurting students, so Kaidan let loose with his full biotic abilities, and wound up killing the guy. Which explains why Kaidan is so controlled, normally.
Shepard: Is there something I can do to help you get over it?
Kaidan: I'm thirty-two, Shepard. You don't serve as long as I have without coming to terms with yourself.
Shepard also has a long heart-to-heart with Liara about her mother - Liara chooses to remember Benezia as she was before this whole Saren thing, which is probably a smart move. And then Liara makes a rather awkward attempt to flirt, which Shepard rather awkwardly has to turn down, explaining that she already has a thing with Kaidan. Awkward turtles all around. Shep bids a hasty retreat.
Shepard chats with Garrus for a while, and he brings up the one that got away during his first year on the job at C-Sec, a salarian geneticist who was doing horrible experiments on living subjects (mostly growing new organs inside people and then harvesting them). Garrus was never able to catch him. I'll sum up this subplot now: Shep manages to track the guy down, and she talks Garrus into arresting him instead of murdering him. The guy freaks out and tries to kill them, and winds up dead anyway, and Shep manages to convince Garrus that even though the result was the same, trying to do it right was worthwhile. Oh, and I'm just going to leave this picture here without further explanation because it is quite possibly the best dialogue wheel choice ever. Ever.

So.
Shep talks with Ashley for a long time about her sisters and her family in general - she once travelled an extremely long distance just to walk her little sister to school. Ashley then quotes some of her dad's favourite poem, Tennyson's "Ulysses", and Shep teases her for liking something sensitive.
Wrex also gets a subplot - he talks about how he and his father found themselves on the opposite sides of a tough situation. His father, a Warlord, wanted to wage war on other tribes. Wrex knew their tribe's numbers were too depleted by the genophage (remember that bioweapon I mentioned earlier?) to risk internecine warfare, but his father saw that hesitation and focus on recovery as cowardice. His father invited him to a "crush", a talk on neutral ground, and, getting into the diplomatic spirit of things, tried to have him murdered. In return, Wrex killed his father. Ouch. In any case, now Wrex has promised his grandfather to recover his family's battle armor, which was taken by the turian military. Enter Shepard! She finds it and recovers it. That's... that's pretty much the entire subplot. But it makes Wrex happy, so that's good.
Meanwhile, Tali's doing better, getting used to the quiet ship. She talks about how her father is an important member of the Admiralty Board (the five-person board that essentially runs the quarian government), and about how she's often been made a target by her father's enemies. She's also under a lot of pressure for her Pilgrimage, which is part of why she's signed on with Shepard.
Enough chit-chat! Back to the Citadel!

Aaand you know it's gonna be a good visit when the first person you run into is Conrad Verner.
Yup, Shep's fanboy is back. This time, he has a proposition: Shepard should sign him on as a Spectre! "I'd make a great Spectre!" Very carefully, Shepard manages to disabuse him of that notion, and he trudges off, looking rather downcast. Sorry, Conrad. You're neither the hero this universe needs nor the one it deserves.
And then it's off to get yelled at by Udina for a while. "Fine! I'll just tell everyone we figured it was a good idea to release a fertile rachni queen in the wilds of Noveria. I'm sure nobody will have a problem with that." Oh, Udina, your sarcasm level is maxed out today, and I kind of love it. Understandably, Shep gets fed up and leaves the Citadel to go do a few more subplots, mostly consisting of getting lured into traps by geth and cultists and such. All in a day's work.
And then we're on to more chats with the crew, where Garrus brings up a concern about Saren: that maybe, after he's caught, he'll find some way to manipulate the Council again to get himself off the hook. Shep and Garrus have a little talk about justice, with Shep taking the very Paragon-y approach of "we do it by the book or we're no better than he is". Garrus seems unconvinced, but says he'll think about it.
Kaidan and Shep flirt some more, which for them includes a lot of talking about apocalyptic futures and galactic politics. You know, romancey stuff. Kaidan is nervous about laying his burdens down on Shepard, and she tries to get him to loosen up a little, assuring him that she's not about to fail at saving the galaxy just because she worries about him from time to time.
Going to visit Ash, Shep finds her celebrating Armistice Day, the day twenty-six years ago when the First Contact War ended. Well, not really celebrating. Remember how Ash was being all elusive when it came to her family's history in the Alliance? Turns out she's the granddaughter of the commander of the garrison at Shanxi - that is, the only human to ever have surrendered to an alien force. As a result, Ash has been getting crap assignments all her career - and this goes to show how stubborn she is, because hey, let's choose the career path where my family name is blacklisted, that'll be fun! But she's determined to regain some honor for her name.
Wrex and Shepard then clash a little over the krogan people. Wrex admits that he "gave up on fighting for a lost cause," and Shep suggests that maybe all isn't lost, that people like Wrex could do a lot of good if they stopped only looking out for number one. Wrex is unconvinced. "I don't like people relying on me, and I bloody well don't like relying on them."
Finally, Tali has a favour to ask - she wants a copy of the geth data Shepard recently recovered, as an extremely valuable gift for her Pilgrimage. Shep is fine with it, and Tali is grateful, and tells Shepard that the only thing she can offer in return is what Shepard already had: Tali's support right to the end of this whole thing with Saren. Aww.
After all this talking, it's time for the final planet on that plotty bullet-point list! Feros is that colony that mysteriously went silent after some geth sightings in the area.

Possibly the geth were just passing through to take pictures of all the pretty scenery. Okay, maybe not. They may, however, have been interested in the two-thirds of Feros that's covered in Prothean ruins. That might be relevant.
Shepard and her team take out some geth and make their way to the colony, Zhu's Hope, where the security force has set up a little bunker and is juuust managing to hold out. More geth attack, Shep takes them out, rinse and repeat a few times. After going around and talking to some of the colonists (and also doing things like solving water and power supply shortages, because this is Shepard, after all), a weird pattern emerges: any time Shepard asks about the colony, the colonists all just tell her to ask Fai Dan, the man in charge. She can't seem to get individual opinions from anyone. Weird.
Anyway, Shepard decides to check out the nearby ExoGeni headquarters - ExoGeni is a company that's been looking at the rare artifacts scattered among the Prothean ruins near the colony. Luckily, there's a handy Mako to drive there. En route, Garrus picks up some chatter on the communications channel - it sounds like people trying to stay hidden nearby.

"Is... is that a drunken rhino driving by? Because it sounds like a drunken rhino."(I'm sorry, Mako, I love you but you're so easy to mock)
Upon investigating, our heroes do indeed find a little hideaway and stop to chat with the people hiding out there - the upshot is that one of the folks hiding in there is missing a daughter, Lisbeth, who works at ExoGeni and hasn't been back since the geth attack. Shepard agrees to keep an eye out for her. Sure enough, once they finally get to Exogeni headquarters, Shepard and her squad find Lisbeth. Or, uh, she finds them and nearly shoots Shepard by accident.

...oops?
But there's no harm done, beyond some athletic leaps into action. Lisbeth dances around the issue a bit, then admits that the geth are probably after the Thorian, an indigenous species that ExoGeni's been studying. There's a big barrier in the way, being powered by a geth ship, so Shepard's approach is to unplug the geth ship, essentially. By blowing stuff up, of course. There's a very funny moment where Shepard is sneaking up behind a krogan trying to access encrypted files on a computer.
Krogan: Damn it! Tell me what I want or I'll blast your virtual ass into actual dust.
Computer: Please contact your supervisor for a level 4 security exemption, or make an appointment with-
Krogan: Stupid machine!
Computer: If there is nothing else, please step aside. There is a queue forming behind you for the use of this console.
There's an awkward pause as the krogan turns around and sees Shepard. And a battle ensues.

This is a picture of me trying to get code to compile on a Monday morning.
Shepard manages to charm the computer, using a borrowed security pass, into telling her more about the Thorian - apparently it's a plant that's exhibited signs of sentience. And, uh, if anyone inhales its spores, it can control them. That probably isn't good. The computer also refers to "the Zhu's Hope control group". Yeeeah, so ExoGeni's been doing creepy sentient plant mind-control experiments on the colonists without their knowledge. That definitely isn't good. And explains the general weird vibe about the colony earlier. I mean, "creepy sentient plant mind-control" is pretty much the definition of a weird vibe.
And hey, remember Lisbeth, the ExoGeni employee who almost shot Shepard earlier? She must have been in on this whole thing. Shep confronts her, and Lisbeth admits that she did know about it - she stuck around after the geth attack to try to send a report to Colonial Affairs, which miiiight fall under the category of "too little, too late", there. Eager to help in any way possible, she offers to come with them back to the colony.
On the way there, passing the hidey-hole they explored earlier, they hear Lisbeth's mom trying to make a transmission, which gets cut off. After dealing with a real jerk of a would-be entrepreneurial ExoGeni employee, who's a little panicked at being found out, Shepard manages to restore order. Shepard's going to try and take out the Thorian without harming the colonists.

Of course, these guys are wandering around as well, which makes it tricky to tell who's a possessed colonist and who's a... whatever this guy is.
But hey, it's Shepard, and she... delicately and carefully fights her way through the colonists without killing any of them, until she reaches Fai Dan, who shoots himself to keep from hurting anyone else. Shepard, Kaidan, and Garrus then take a stroll down into the catacombs under the colony, where the Thorian lives, and kill it, rescuing an asari, Shiala, who'd been trapped inside it the whole time. Shiala tells them that Saren found out that the Thorian had knowledge of a Cipher that would enable him to get his own creepy-nightmare-vision sorted out (remember when he was hovering by the Prothean beacon, way back when? Yup, same experience as Shepard had). So Saren traded Shiala for the Cipher, which was pretty much not cool in Shiala's books, so Shiala's pretty okay with helping Shepard take Saren down. She does so by also giving Shepard the Cipher, which triggers another incoherent, creepy nightmare-vision of incoherent creepiness.
It still doesn't make any more sense to Shepard, but apparently the ancestral memories of the Protheans are part of her now, and she'll be able to slowly process that vision and make sense of it. Kaidan is concerned and insists they go back to the ship.

Hey, we haven't had a group meeting in a while!
Liara offers to help Shepard recover from the nightmare-vision thing with a sort of mind meld so they can compare notes on the whole experience. More nightmarish flashes that don't make any more sense to me, but apparently Liara can decipher enough to figure out that the beacon on Eden Prime must have been badly damaged, which is why we're only getting bits and pieces of this warning. Given that said beacon is 50,000 years old, I'll buy that explanation. Liara can't figure anything new from these bits and pieces of information, and deduces that Saren must have found another beacon in order to fill in the blanks. She then nearly keels over again, which at this point is the traditional signal to adjourn group meetings.
Shep calls up the Council, who are annoyed at how Shepard destroyed the Thorian, accusing her of doing it just to save the human colony. Shepard insists that she would've saved the colonists even if they hadn't been human, which the salarian councilor deems admirable. But he reminds her that Spectres sometimes have to be prepared to make sacrifices.

Was... was that a dramatic chord of foreshadowing, there?
More crew conversations ensue! Kaidan and Shep flirt and talk about how it feels like they're getting closer to heart of all this, possibly because they've realized we've now visited all three places on that bullet-point list above; Garrus figures out the difference between justice and personal revenge and decides to try to become a Spectre again, this time doing it without compromising himself or sacrificing innocents; Ash admits to being a little surprised at how smoothly Shepard handled the situation with ExoGeni (basically convincing them that advertising the colony as survivors-against-all-odds will bring in more investors and more money); Wrex tells a great story about an asari commando/mercenary who was his biggest rival and the person he admired most; and Tali tells Shepard how proud she is to have been a part of this journey so far.
And then it's back to the Citadel, where Udina is beyond sarcasm at this point and is just openly frustrated at Shepard's not-so-politically-savvy flailing around the galaxy. "Just ignore him, Shepard," is Anderson's not-so-politically-savvy advice. Another couple of subplots ensue, and then the Council calls the Normandy directly with big news: a salarian "infiltration regiment" (i.e., spies) on the planet Virmire have been gathering intel on Saren. If you've played the game before, you just flinched at the word "Virmire", didn't you? Anyway, our salarian spies tried to send the Council a high-priority message - it just came through as static, but it was on an extremely important frequency - so they must know something. Shepard agrees to check it out.

To Virmire!
The geth are hanging around Virmire in force, so Joker drops the Mako in hot and pulls the Normandy back to keep her safe until the nearby anti-aircraft guns are taken offline. A bunch of Mako-driving and geth-defeating ensues, and the guns are finally taken offline, so the Normandy manages to touch down at the salarians' base. Shepard meets the guy in charge of this Special Tasks Group, a Captain Kirrahe, who informs them that they've just landed in a hot zone. Apparently when they landed the Normandy, they managed to alert every anti-aircraft gun for hundreds of miles around, which means they're effectively grounded. Whoops.
So what's the plan, according to Kirrahe? "We stay put until the Council sends the reinforcements we requested." There's an awkward pause, until Kaidan pipes up with, "We are the reinforcements." Apparently Kirrahe asked for a whole fleet, but hey, all the Council got was static. Greeeat.

Well, this is certainly awkward.
Kirrahe reveals that they've intercepted geth communications about Saren - this is his facility, no doubt about that, which is why they wanted a whole fleet to come in and take it down. Apparently Saren's been using this facility to breed an army of krogan, which catches Wrex's attention - after all, the genophage bioweapon was supposed to have nearly sterilized them, making only one in a thousand pregnancies viable. Apparently, Saren has discovered a cure for the genophage. (So maybe this whole inadvertently-doing-amazing-things schtick is a Spectre thing, not just a Shepard thing. "Jeez, I just wanted a personal army, and I accidentally cured a genocidal disease. Again.")
So Kirrahe suggests that destroying the super-soldier factory might be a good plan. Wrex emphatically disagrees - the cure for his people, for the entire krogan race, is contained in that facility.

"We cannot make the same mistake again-" "We are not a mistake."
Wrex stalks off to go do the krogan equivalent of skipping stones in the nearby lake, which involves idly shooting his shotgun in its general direction.

I just really like the composition of this whole scene. Virmire's pretty, you've gotta give it that.
Shepard goes to talk to Wrex, who is... not happy. He is, in fact, extremely angry. He gave up on his people years ago, and you can tell that Shepard's been getting him hoping again - and then he gets this chance at redemption, only to have it taken away. No wonder he's mad. Shep tries to remind him that Saren's the enemy here, and he points out that Saren's the one with the cure. "Help me out here, Shepard. The lines between friend and foe are getting a little blurry, from where I stand." Shepard jumps in and tells him it's not a cure, it's a weapon, and if Saren wins, the krogan won't be around to reap the benefits. It's a zero-sum-game for organic life in general. But Wrex figures it's worth the risk.

"This is the fate of my entire people we're talking about!"
And Wrex pulls a weapon, which means Shep pulls a weapon, instinctively. Things are getting tense! So Shepard straightens up, lowers her weapon, and reminds Wrex that Saren's krogan are not his people - they'd just be slaves, tools.

It takes a lot of badassery to lower your weapon when faced with an angry krogan. Just saying.
Wrex thinks about it, then visibly pulls himself together. "All right, Shepard. You've made your point. I don't like this, but I trust you enough to follow your lead."
Yeah, so obviously this could have gone a lot differently - if you're not enough of a paragon to argue your case, or enough of a renegade to bully Wrex into accepting your decision, you wind up having to kill him here. Virmire is ever such a fun planet, isn't it?
Meanwhile, Kirrahe has come up with a plan to assault Saren's base. He's decided to convert part of his ship into a nuke - unfortunately, it can't just be dropped from orbit, as the facility's too well-fortified, so it'll have to be placed in position. Kirrahe's plan is to have the Normandy drop off the bomb, but the STG team will have to go in on foot and pacify resistance, as well as knock out those dang AA guns. Going in on foot is pretty much suicidal, but Kirrahe is confident that his teams will be able to provide enough of a diversion that Shepard's shadow team can sneak around back and get in position to receive the nuke. "We're tougher than we look, Commander. But it's true, I don't expect many of us will make it out alive. And that makes what I'm going to ask even more difficult. I need one of your men to accompany me, to help coordinate the teams."

Being the Big Damn Heroes that they are, Kaidan and Ash immediately start arguing over who gets to volunteer for this incredibly risky mission.
Shepard decides to send Ashley. "No heroics, understood?" Everyone parts ways, a little shakily.
Kaidan: We'll be fine. You'll see.
Ashley: Yeah, I just- Good luck.
The Normandy crew has an exit strategy in the form of, well, the Normandy, but the salarians are basically planning to try and outrun the blast. Yikes. These guys are pretty epic badasses. And then Kirrahe gives a speech, which is unexpectedly inspiring, all about how the salarians' greatest heroes are the ones whose names are least known. "We are trained for espionage. We would be legends, but the records are sealed."
And on that note, Shepard's shadow team (Shep, Kaidan, and Wrex) head out. They keep focused, but also find a few opportunities to make life easier for Kirrahe's teams. They find some salarians Saren has been experimenting on - he's apparently exploring how indoctrination works (remember Benezia talking about how hanging around Saren's ship for long enough makes you want to be his BFF?). Shepard releases the remaining test subjects, some of whom snap and attack, and others of whom manage to keep it together enough to make a run for it.
Our heroes then meet Rana Thanoptis, an asari who's been working with Saren on his indoctrination research. She's come to the realization that this job isn't worth dying over.

Showing remarkable self-restraint, Shepard does not make the obvious pun about a killer severance package.
Rana gives them full access to all of Saren's personal files, trying to barter for her escape. She tells them that Saren's ship, Sovereign, emits some sort of signal that Saren's been using to influence his followers and control them. Shepard asks the obvious question - if it's working out so great for him, why is Saren researching indoctrination? Rana says that she's not sure if Saren is really in control of the signal. "I think... he's scared it might be affecting him."
Shepard lets her go. Sort of. "I'm gonna blow this place to hell and gone. If you want to make it out alive, you'd better start running."
A quick elevator ride later, Shepard finds... another beacon, like the one on Eden Prime. Again with the hovering and the nightmarish visions, only this time, instead of the beacon exploding and Shepard keeling over, she opens her eyes, apparently in understanding. I gotta say, it still looks like a bunch of random stock footage to me, but hey, I don't have the Cipher, do I?Must be DLC.
On the way out, some glowy red lights appear, in the shape of Sovereign, Saren's ship, the creepy lightning glove thing.

And Wrex notes, astutely, "I get the feeling something bad is about to happen."
And Sovereign starts talking, in a creeeeepy voice, and calling them names like "rudimentary creatures of blood and flesh, you touch my mind, fumbling in ignorance, incapable of understanding". Yeah? Well... well, so's your mom!
So Sovereign brags for a while about how far beyond their comprehension it is. Shepard states the obvious: "Sovereign isn't just some Reaper ship Saren found. It's an actual Reaper!" Sovereign starts name-dropping, all, "Yeah, we totally killed the Protheans that one time." The general notion is that organic life is kind of an accident, and synthetic life is the pinnacle of existence. As soon as organic life becomes advanced enough, the Reapers charge in and destroy it, for reasons that Sovereign suggests are all cosmic and unknowable, but which I suspect probably boil down to "if they become strong enough, they will try to destroy us because that's what organics do to synthetics." I bet Sovereign roots for the Cylons when it watches BSG.
But Sovereign keeps dropping the plot bombs. "The Protheans were not the first. They did not create the Citadel. They did not forge the mass relays. They merely found them."
So hey, the Reapers built the mass relays for other civilizations to find, to force them to develop along the paths the Reapers desired, while they bided their time out in the dark space between galaxies. Presumably watching TV and ordering pizza from Andromeda.

Blah blah blah, "we impose order on the chaos of organic evolution", yadda yadda, "we're awesome".
Kaidan clues in to the whole "Reaper" name and realizes organic life is being harvested. Sovereign gets a little vague about what they actually want all this organic life for, then rambles about how each Reaper is a nation, "independent, free of all weakness". Thewriters Reapers are wise and unknowable. Rather optimistically, Shep asks if Sovereign is the last of his kind. "We are legion. The time of our return is coming. Our numbers will darken the sky of every world." Oh. So that'd be a no, then.
Shepard is all, "Yeah, whatever, I'll just blow you guys up." Sovereign is remarkably unfazed. "I am the vanguard of your destruction. This exchange is over." And he disappears.
Joker calls in to warn them that Sovereign - actual Sovereign, not holographic and vaguely menacing Sovereign - is heading straight for Shepard. Time to set the nuke!
More fighting with the geth, more activating and deactivating all the relevant guns and switches. They manage to take down the anti-aircraft turret. Shepard gets her team to the rendezvous point, and Joker flies the Normandy into position.

Special delivery for a Commander Shepard: one nuke, hella big.
The nuke's in position and almost ready when Ashley calls Shepard up. Apparently the geth have them pinned down in the AA tower, and the team won't make it to the rendezvous point in time for pickup by the Normandy. Kaidan points out that it'll take a few minutes to finish arming the bomb anyway, so Shepard's got time to run over and try to help. She sets off with Wrex and Garrus, leaving Kaidan to take care of the bomb.

You know, these epic race-against-time scenes are somewhat undercut by all the awkward elevator rides.
And... the geth send reinforcements over to where Kaidan's trying to set up them the bomb. Everyone strikes a dramatic pose, and Shepard asks if Kaidan can hold them off. He thinks not, and activates the bomb, to make sure it goes off no matter what. "It's done, Commander. Go get Williams, and get the hell out of here."
Aaaaaand this happens:

Ouch.
Shepard decides to rescue Kaidan. "I'm sorry, Ash. I had to make a choice." "I understand, Commander. That's the whole point of this game." (Okay, she doesn't actually say that.) So Shepard rushes back to rescue Kaidan, who's been injured and is trying to keep the geth away from the nuke. And Saren himself makes an appearance.

O HAI.
Shepard tries shooting him, but it just reflects off a super-strong barrier of some sort. Saren reveals that he's mostly helping the Reapers because he doesn't see any other choice. "The Protheans tried to fight, and they were utterly destroyed." He thinks surrender might be organic life's only hope of survival, so he's getting in on the ground floor. Shepard points out that the Reapers probably aren't gonna be big on letting them live. Saren thinks it's worth the risk, if it could mean saving trillions of lives.
He says that after he joined up with Sovereign, he created this facility to try to protect himself from indoctrination. Shepard catches the uncertainty in his posturing - "You're afraid Sovereign's influencing you. You're afraid he's controlling your thoughts." Saren shrugs it off, unconvincingly, asserting that he'd notice if it were happening.
Shep tries to get Saren to tell her about the Conduit, suggesting that they could work together to defeat Sovereign using it. He doesn't give much away. "Sovereign needs my help to find it. That is the only reason I have not been indoctrinated." Yeeeeah, Saren, buddy? That doesn't sound like a very tenable position.
Shepard keeps pushing the message that there's another option - not just submission or extinction - in the form of resistance. "I no longer believe that, Shepard." But Saren... doesn't quite sound convinced anymore. He claims he's trying to forge an alliance between organics and machines.
And then he realizes he's been monologuing for a while and decides to get on with killing Shepard to keep her from dooming their entire civilization.

Now, where were we? Oh, right, homicidal rage.
The fight does not go well for Shepard, who gets pretty beat up, but the alarm warning on the bomb starts sounding, which is all the distraction Shep needs to punch Saren in the face. He makes a run for it, and she's too blurry-eyed to shoot him as he retreats. Instead, she grabs Kaidan and retreats to the Normandy.

And the Normandy makes it out in the nick of time.
On to Part Three (in which there are lots and lots and lots of explosions)
Okay, things are getting a little tangled right now, so feel free to go back to those handy bullet points in the first post. We've visited the Artermis Tau cluster and found Liara, so that's one out of three completed. Enough with these subplots; on to the next plot world! To Noveria! It's a corporate-owned planet, and a blizzard is raging as our heroes arrive.
There's a bit of a misunderstanding over weapons and who gets to carry them, but eventually Shepard manages to get to the heart of this particular plot world: Matriarch Benezia is here. Right now. With, apparently, a mysterious cargo and a bunch of commandos in tow. Unfortunately, she went up to a research station that's been made inaccessible by air due to the storm, and getting a garage pass to use ground transport is a bit of a hassle that involves taking down the corrupt administrator of the place, winning a firefight in an office, exposing dirty cops, and saving two people's careers.

Again, this is why nobody ever asks Shepard to do normal things, like picking up some milk at the store. "Oh, and on the way, I ran into this supervillain who's been using the milk to build a nuclear weapon, so I stopped him and rescued the twelve puppies he'd kept trapped in his basement. You wanted 2%, right?"
Shepard finally gets to the garage... and she's promptly attacked by geth. After taking them out, our heroes realize they must've been smuggled in via Benezia's cargo containers. Sneaky. And off we go, to the Peak 15 research station!

This is the best part of the Mako: if you're in a hurry, you can totally just drive over everything in your path. MAKO SMASH.
Upon reaching the station, Shepard and company run into some creepy bug things that instantly attack. Apparently, they're rachni. Whaaaaaat. The rachni, remember, are the ultra-agressive race the krogan fought to extinction a thousand years back. Not "nearly to extinction". These guys were gone-zo. So it's understandably baffling to have them suddenly trying to chew off your face.

Ouch. Has... has anyone tried telling them they're not supposed to exist? That might work.
There's another digression while our heroes try to get the research station operational again (it's in "holy-crap-panic" mode, with everything shut down), which includes the line:
Virtual Assistant: It looks like you're trying to restore this facility. Would you like help?
So, yeah, Clippy still exists in the future.
Anyway. Our heroes fight their way through the rachni, argue with computers for a while, and eventually get everything up and running again, which lets them take a tram to where a bunch of scientists and security personnel are holed up. After a great deal of waffling about nondisclosure agreements, the scientists admit that they've been running experiments on a rachni egg that was discovered in cryo-suspension aboard a ship - the egg hatched unexpectedly (it was a thousand years old, after all), and turned out to contain a rachni queen. She was used to breed weaponized "soldiers" - mindless killing machines - for use as weapons. Aaand this all came back to bite everyone in the ass when the mindless killing machines got loose and started, er, mindlessly killing.
While investigating all this, Shepard more-or-less accidentally manages to cure a plague and expose a sleeper agent for Benezia. As you do. Eventually, our heroes find Benezia and confront her, which is an awkward family reunion for Liara, since her mom immediately starts trying to kill her.

Mostly I just like the dramatic lighting in this shot.
Conveniently, after all her associates are dead, Benezia has a jolt of self-awareness and seems to come back to herself. She talks a bit about Saren's really creepy giant gloved lightning hand starship, which apparently the geth didn't build - she doesn't know where it came from. But the longer you stay on the ship, the more awesome Saren seems, and the more you want to hang out with him and, you know, kill people for him and stuff. Benezia has managed to seal part of her mind away from this indoctrination, temporarily, which is how she's able to communicate now.
She reveals that Saren is looking for the Mu Relay, which apparently is what'll lead him to that all-important Conduit, whatever it is - this relay been lost for millennia, but the rachni have this cross-generational memory thing going, and so Benezia was sent to get the information from the rachni queen. She sent the coordinates to Saren already, but manages to give a copy to Shep. But that's only part of the story - without knowing Saren's final destination, the location of the relay itself is useless (it's like knowing the location of an airport, rather than the final destination). But it's better than wandering aimlessly and taking on random subplots.
But Benezia loses control again, and Shep is forced to kill her before she can kill them. Poor Liara is pretty traumatized by the whole thing. This game really likes breaking its characters.

Also, her mom's last words are "No light? They always said there would be a-", which is not exactly reassuring.
After Benezia dies, Shepard goes over to check out the rachni queen, and... one of Benezia's dead associates goes all possessed-zombie and staggers over to say hi.

Braaaaains... I mean, 'sup?
Turns out that's the only way the rachni queen can communicate, and she still communicates in a very confusing/poetic way. "This one serves as our voice. We cannot sing. Not in these low spaces. She has colours we have no name for." Think of them as the, uh, zombie-possessing beat poets of the Mass Effect universe. *snap snap*
Anyway, the rachni queen eventually manages to get across that she doesn't really know what the heck happened with the whole rachni war thing since she was just an egg at the time, and that in this instance, her children have essentially been kept away from her and have been programmed to be mindless killing machines and need to be destroyed. All in all, she seems like a pretty decent giant bug alien, so Shepard, with a sneaking suspicion that this is gonna come back to bite her in the ass in some later game, decides to let her go. (This, by the way, is one of the major Paragon decisions of the game - the Renegade option is to kill the rachni queen.)
Back to the Normandy, to report to the Council, who are understandably a little vexed that Shepard has let the rachni queen go, given how the rachni almost took over the galaxy that one time. Juuust a little vexed. Since this is pretty much the Council's default reaction to Shepard, she's largely unfazed.
Time for another crew conversation? I think so! Shepard does some more serious flirting with Kaidan, and there's an awkward conversation where Kaidan's all "Uh, but I thought you and Liara were-". But nope, this is a Shepard/Kaidan playthrough, so they do some more flirting. They really are kind of adorable.

D'awww.
Kaidan reveals a seriously bad bit of his past, at the school for biotics he attended - one of his instructors snapped and started hurting students, so Kaidan let loose with his full biotic abilities, and wound up killing the guy. Which explains why Kaidan is so controlled, normally.
Shepard: Is there something I can do to help you get over it?
Kaidan: I'm thirty-two, Shepard. You don't serve as long as I have without coming to terms with yourself.
Shepard also has a long heart-to-heart with Liara about her mother - Liara chooses to remember Benezia as she was before this whole Saren thing, which is probably a smart move. And then Liara makes a rather awkward attempt to flirt, which Shepard rather awkwardly has to turn down, explaining that she already has a thing with Kaidan. Awkward turtles all around. Shep bids a hasty retreat.
Shepard chats with Garrus for a while, and he brings up the one that got away during his first year on the job at C-Sec, a salarian geneticist who was doing horrible experiments on living subjects (mostly growing new organs inside people and then harvesting them). Garrus was never able to catch him. I'll sum up this subplot now: Shep manages to track the guy down, and she talks Garrus into arresting him instead of murdering him. The guy freaks out and tries to kill them, and winds up dead anyway, and Shep manages to convince Garrus that even though the result was the same, trying to do it right was worthwhile. Oh, and I'm just going to leave this picture here without further explanation because it is quite possibly the best dialogue wheel choice ever. Ever.

So.
Shep talks with Ashley for a long time about her sisters and her family in general - she once travelled an extremely long distance just to walk her little sister to school. Ashley then quotes some of her dad's favourite poem, Tennyson's "Ulysses", and Shep teases her for liking something sensitive.
Wrex also gets a subplot - he talks about how he and his father found themselves on the opposite sides of a tough situation. His father, a Warlord, wanted to wage war on other tribes. Wrex knew their tribe's numbers were too depleted by the genophage (remember that bioweapon I mentioned earlier?) to risk internecine warfare, but his father saw that hesitation and focus on recovery as cowardice. His father invited him to a "crush", a talk on neutral ground, and, getting into the diplomatic spirit of things, tried to have him murdered. In return, Wrex killed his father. Ouch. In any case, now Wrex has promised his grandfather to recover his family's battle armor, which was taken by the turian military. Enter Shepard! She finds it and recovers it. That's... that's pretty much the entire subplot. But it makes Wrex happy, so that's good.
Meanwhile, Tali's doing better, getting used to the quiet ship. She talks about how her father is an important member of the Admiralty Board (the five-person board that essentially runs the quarian government), and about how she's often been made a target by her father's enemies. She's also under a lot of pressure for her Pilgrimage, which is part of why she's signed on with Shepard.
Enough chit-chat! Back to the Citadel!

Aaand you know it's gonna be a good visit when the first person you run into is Conrad Verner.
Yup, Shep's fanboy is back. This time, he has a proposition: Shepard should sign him on as a Spectre! "I'd make a great Spectre!" Very carefully, Shepard manages to disabuse him of that notion, and he trudges off, looking rather downcast. Sorry, Conrad. You're neither the hero this universe needs nor the one it deserves.
And then it's off to get yelled at by Udina for a while. "Fine! I'll just tell everyone we figured it was a good idea to release a fertile rachni queen in the wilds of Noveria. I'm sure nobody will have a problem with that." Oh, Udina, your sarcasm level is maxed out today, and I kind of love it. Understandably, Shep gets fed up and leaves the Citadel to go do a few more subplots, mostly consisting of getting lured into traps by geth and cultists and such. All in a day's work.
And then we're on to more chats with the crew, where Garrus brings up a concern about Saren: that maybe, after he's caught, he'll find some way to manipulate the Council again to get himself off the hook. Shep and Garrus have a little talk about justice, with Shep taking the very Paragon-y approach of "we do it by the book or we're no better than he is". Garrus seems unconvinced, but says he'll think about it.
Kaidan and Shep flirt some more, which for them includes a lot of talking about apocalyptic futures and galactic politics. You know, romancey stuff. Kaidan is nervous about laying his burdens down on Shepard, and she tries to get him to loosen up a little, assuring him that she's not about to fail at saving the galaxy just because she worries about him from time to time.
Going to visit Ash, Shep finds her celebrating Armistice Day, the day twenty-six years ago when the First Contact War ended. Well, not really celebrating. Remember how Ash was being all elusive when it came to her family's history in the Alliance? Turns out she's the granddaughter of the commander of the garrison at Shanxi - that is, the only human to ever have surrendered to an alien force. As a result, Ash has been getting crap assignments all her career - and this goes to show how stubborn she is, because hey, let's choose the career path where my family name is blacklisted, that'll be fun! But she's determined to regain some honor for her name.
Wrex and Shepard then clash a little over the krogan people. Wrex admits that he "gave up on fighting for a lost cause," and Shep suggests that maybe all isn't lost, that people like Wrex could do a lot of good if they stopped only looking out for number one. Wrex is unconvinced. "I don't like people relying on me, and I bloody well don't like relying on them."
Finally, Tali has a favour to ask - she wants a copy of the geth data Shepard recently recovered, as an extremely valuable gift for her Pilgrimage. Shep is fine with it, and Tali is grateful, and tells Shepard that the only thing she can offer in return is what Shepard already had: Tali's support right to the end of this whole thing with Saren. Aww.
After all this talking, it's time for the final planet on that plotty bullet-point list! Feros is that colony that mysteriously went silent after some geth sightings in the area.

Possibly the geth were just passing through to take pictures of all the pretty scenery. Okay, maybe not. They may, however, have been interested in the two-thirds of Feros that's covered in Prothean ruins. That might be relevant.
Shepard and her team take out some geth and make their way to the colony, Zhu's Hope, where the security force has set up a little bunker and is juuust managing to hold out. More geth attack, Shep takes them out, rinse and repeat a few times. After going around and talking to some of the colonists (and also doing things like solving water and power supply shortages, because this is Shepard, after all), a weird pattern emerges: any time Shepard asks about the colony, the colonists all just tell her to ask Fai Dan, the man in charge. She can't seem to get individual opinions from anyone. Weird.
Anyway, Shepard decides to check out the nearby ExoGeni headquarters - ExoGeni is a company that's been looking at the rare artifacts scattered among the Prothean ruins near the colony. Luckily, there's a handy Mako to drive there. En route, Garrus picks up some chatter on the communications channel - it sounds like people trying to stay hidden nearby.

"Is... is that a drunken rhino driving by? Because it sounds like a drunken rhino."(I'm sorry, Mako, I love you but you're so easy to mock)
Upon investigating, our heroes do indeed find a little hideaway and stop to chat with the people hiding out there - the upshot is that one of the folks hiding in there is missing a daughter, Lisbeth, who works at ExoGeni and hasn't been back since the geth attack. Shepard agrees to keep an eye out for her. Sure enough, once they finally get to Exogeni headquarters, Shepard and her squad find Lisbeth. Or, uh, she finds them and nearly shoots Shepard by accident.

...oops?
But there's no harm done, beyond some athletic leaps into action. Lisbeth dances around the issue a bit, then admits that the geth are probably after the Thorian, an indigenous species that ExoGeni's been studying. There's a big barrier in the way, being powered by a geth ship, so Shepard's approach is to unplug the geth ship, essentially. By blowing stuff up, of course. There's a very funny moment where Shepard is sneaking up behind a krogan trying to access encrypted files on a computer.
Krogan: Damn it! Tell me what I want or I'll blast your virtual ass into actual dust.
Computer: Please contact your supervisor for a level 4 security exemption, or make an appointment with-
Krogan: Stupid machine!
Computer: If there is nothing else, please step aside. There is a queue forming behind you for the use of this console.
There's an awkward pause as the krogan turns around and sees Shepard. And a battle ensues.

This is a picture of me trying to get code to compile on a Monday morning.
Shepard manages to charm the computer, using a borrowed security pass, into telling her more about the Thorian - apparently it's a plant that's exhibited signs of sentience. And, uh, if anyone inhales its spores, it can control them. That probably isn't good. The computer also refers to "the Zhu's Hope control group". Yeeeah, so ExoGeni's been doing creepy sentient plant mind-control experiments on the colonists without their knowledge. That definitely isn't good. And explains the general weird vibe about the colony earlier. I mean, "creepy sentient plant mind-control" is pretty much the definition of a weird vibe.
And hey, remember Lisbeth, the ExoGeni employee who almost shot Shepard earlier? She must have been in on this whole thing. Shep confronts her, and Lisbeth admits that she did know about it - she stuck around after the geth attack to try to send a report to Colonial Affairs, which miiiight fall under the category of "too little, too late", there. Eager to help in any way possible, she offers to come with them back to the colony.
On the way there, passing the hidey-hole they explored earlier, they hear Lisbeth's mom trying to make a transmission, which gets cut off. After dealing with a real jerk of a would-be entrepreneurial ExoGeni employee, who's a little panicked at being found out, Shepard manages to restore order. Shepard's going to try and take out the Thorian without harming the colonists.

Of course, these guys are wandering around as well, which makes it tricky to tell who's a possessed colonist and who's a... whatever this guy is.
But hey, it's Shepard, and she... delicately and carefully fights her way through the colonists without killing any of them, until she reaches Fai Dan, who shoots himself to keep from hurting anyone else. Shepard, Kaidan, and Garrus then take a stroll down into the catacombs under the colony, where the Thorian lives, and kill it, rescuing an asari, Shiala, who'd been trapped inside it the whole time. Shiala tells them that Saren found out that the Thorian had knowledge of a Cipher that would enable him to get his own creepy-nightmare-vision sorted out (remember when he was hovering by the Prothean beacon, way back when? Yup, same experience as Shepard had). So Saren traded Shiala for the Cipher, which was pretty much not cool in Shiala's books, so Shiala's pretty okay with helping Shepard take Saren down. She does so by also giving Shepard the Cipher, which triggers another incoherent, creepy nightmare-vision of incoherent creepiness.
It still doesn't make any more sense to Shepard, but apparently the ancestral memories of the Protheans are part of her now, and she'll be able to slowly process that vision and make sense of it. Kaidan is concerned and insists they go back to the ship.

Hey, we haven't had a group meeting in a while!
Liara offers to help Shepard recover from the nightmare-vision thing with a sort of mind meld so they can compare notes on the whole experience. More nightmarish flashes that don't make any more sense to me, but apparently Liara can decipher enough to figure out that the beacon on Eden Prime must have been badly damaged, which is why we're only getting bits and pieces of this warning. Given that said beacon is 50,000 years old, I'll buy that explanation. Liara can't figure anything new from these bits and pieces of information, and deduces that Saren must have found another beacon in order to fill in the blanks. She then nearly keels over again, which at this point is the traditional signal to adjourn group meetings.
Shep calls up the Council, who are annoyed at how Shepard destroyed the Thorian, accusing her of doing it just to save the human colony. Shepard insists that she would've saved the colonists even if they hadn't been human, which the salarian councilor deems admirable. But he reminds her that Spectres sometimes have to be prepared to make sacrifices.

Was... was that a dramatic chord of foreshadowing, there?
More crew conversations ensue! Kaidan and Shep flirt and talk about how it feels like they're getting closer to heart of all this, possibly because they've realized we've now visited all three places on that bullet-point list above; Garrus figures out the difference between justice and personal revenge and decides to try to become a Spectre again, this time doing it without compromising himself or sacrificing innocents; Ash admits to being a little surprised at how smoothly Shepard handled the situation with ExoGeni (basically convincing them that advertising the colony as survivors-against-all-odds will bring in more investors and more money); Wrex tells a great story about an asari commando/mercenary who was his biggest rival and the person he admired most; and Tali tells Shepard how proud she is to have been a part of this journey so far.
And then it's back to the Citadel, where Udina is beyond sarcasm at this point and is just openly frustrated at Shepard's not-so-politically-savvy flailing around the galaxy. "Just ignore him, Shepard," is Anderson's not-so-politically-savvy advice. Another couple of subplots ensue, and then the Council calls the Normandy directly with big news: a salarian "infiltration regiment" (i.e., spies) on the planet Virmire have been gathering intel on Saren. If you've played the game before, you just flinched at the word "Virmire", didn't you? Anyway, our salarian spies tried to send the Council a high-priority message - it just came through as static, but it was on an extremely important frequency - so they must know something. Shepard agrees to check it out.

To Virmire!
The geth are hanging around Virmire in force, so Joker drops the Mako in hot and pulls the Normandy back to keep her safe until the nearby anti-aircraft guns are taken offline. A bunch of Mako-driving and geth-defeating ensues, and the guns are finally taken offline, so the Normandy manages to touch down at the salarians' base. Shepard meets the guy in charge of this Special Tasks Group, a Captain Kirrahe, who informs them that they've just landed in a hot zone. Apparently when they landed the Normandy, they managed to alert every anti-aircraft gun for hundreds of miles around, which means they're effectively grounded. Whoops.
So what's the plan, according to Kirrahe? "We stay put until the Council sends the reinforcements we requested." There's an awkward pause, until Kaidan pipes up with, "We are the reinforcements." Apparently Kirrahe asked for a whole fleet, but hey, all the Council got was static. Greeeat.

Well, this is certainly awkward.
Kirrahe reveals that they've intercepted geth communications about Saren - this is his facility, no doubt about that, which is why they wanted a whole fleet to come in and take it down. Apparently Saren's been using this facility to breed an army of krogan, which catches Wrex's attention - after all, the genophage bioweapon was supposed to have nearly sterilized them, making only one in a thousand pregnancies viable. Apparently, Saren has discovered a cure for the genophage. (So maybe this whole inadvertently-doing-amazing-things schtick is a Spectre thing, not just a Shepard thing. "Jeez, I just wanted a personal army, and I accidentally cured a genocidal disease. Again.")
So Kirrahe suggests that destroying the super-soldier factory might be a good plan. Wrex emphatically disagrees - the cure for his people, for the entire krogan race, is contained in that facility.

"We cannot make the same mistake again-" "We are not a mistake."
Wrex stalks off to go do the krogan equivalent of skipping stones in the nearby lake, which involves idly shooting his shotgun in its general direction.

I just really like the composition of this whole scene. Virmire's pretty, you've gotta give it that.
Shepard goes to talk to Wrex, who is... not happy. He is, in fact, extremely angry. He gave up on his people years ago, and you can tell that Shepard's been getting him hoping again - and then he gets this chance at redemption, only to have it taken away. No wonder he's mad. Shep tries to remind him that Saren's the enemy here, and he points out that Saren's the one with the cure. "Help me out here, Shepard. The lines between friend and foe are getting a little blurry, from where I stand." Shepard jumps in and tells him it's not a cure, it's a weapon, and if Saren wins, the krogan won't be around to reap the benefits. It's a zero-sum-game for organic life in general. But Wrex figures it's worth the risk.

"This is the fate of my entire people we're talking about!"
And Wrex pulls a weapon, which means Shep pulls a weapon, instinctively. Things are getting tense! So Shepard straightens up, lowers her weapon, and reminds Wrex that Saren's krogan are not his people - they'd just be slaves, tools.

It takes a lot of badassery to lower your weapon when faced with an angry krogan. Just saying.
Wrex thinks about it, then visibly pulls himself together. "All right, Shepard. You've made your point. I don't like this, but I trust you enough to follow your lead."
Yeah, so obviously this could have gone a lot differently - if you're not enough of a paragon to argue your case, or enough of a renegade to bully Wrex into accepting your decision, you wind up having to kill him here. Virmire is ever such a fun planet, isn't it?
Meanwhile, Kirrahe has come up with a plan to assault Saren's base. He's decided to convert part of his ship into a nuke - unfortunately, it can't just be dropped from orbit, as the facility's too well-fortified, so it'll have to be placed in position. Kirrahe's plan is to have the Normandy drop off the bomb, but the STG team will have to go in on foot and pacify resistance, as well as knock out those dang AA guns. Going in on foot is pretty much suicidal, but Kirrahe is confident that his teams will be able to provide enough of a diversion that Shepard's shadow team can sneak around back and get in position to receive the nuke. "We're tougher than we look, Commander. But it's true, I don't expect many of us will make it out alive. And that makes what I'm going to ask even more difficult. I need one of your men to accompany me, to help coordinate the teams."

Being the Big Damn Heroes that they are, Kaidan and Ash immediately start arguing over who gets to volunteer for this incredibly risky mission.
Shepard decides to send Ashley. "No heroics, understood?" Everyone parts ways, a little shakily.
Kaidan: We'll be fine. You'll see.
Ashley: Yeah, I just- Good luck.
The Normandy crew has an exit strategy in the form of, well, the Normandy, but the salarians are basically planning to try and outrun the blast. Yikes. These guys are pretty epic badasses. And then Kirrahe gives a speech, which is unexpectedly inspiring, all about how the salarians' greatest heroes are the ones whose names are least known. "We are trained for espionage. We would be legends, but the records are sealed."
And on that note, Shepard's shadow team (Shep, Kaidan, and Wrex) head out. They keep focused, but also find a few opportunities to make life easier for Kirrahe's teams. They find some salarians Saren has been experimenting on - he's apparently exploring how indoctrination works (remember Benezia talking about how hanging around Saren's ship for long enough makes you want to be his BFF?). Shepard releases the remaining test subjects, some of whom snap and attack, and others of whom manage to keep it together enough to make a run for it.
Our heroes then meet Rana Thanoptis, an asari who's been working with Saren on his indoctrination research. She's come to the realization that this job isn't worth dying over.

Showing remarkable self-restraint, Shepard does not make the obvious pun about a killer severance package.
Rana gives them full access to all of Saren's personal files, trying to barter for her escape. She tells them that Saren's ship, Sovereign, emits some sort of signal that Saren's been using to influence his followers and control them. Shepard asks the obvious question - if it's working out so great for him, why is Saren researching indoctrination? Rana says that she's not sure if Saren is really in control of the signal. "I think... he's scared it might be affecting him."
Shepard lets her go. Sort of. "I'm gonna blow this place to hell and gone. If you want to make it out alive, you'd better start running."
A quick elevator ride later, Shepard finds... another beacon, like the one on Eden Prime. Again with the hovering and the nightmarish visions, only this time, instead of the beacon exploding and Shepard keeling over, she opens her eyes, apparently in understanding. I gotta say, it still looks like a bunch of random stock footage to me, but hey, I don't have the Cipher, do I?
On the way out, some glowy red lights appear, in the shape of Sovereign, Saren's ship, the creepy lightning glove thing.

And Wrex notes, astutely, "I get the feeling something bad is about to happen."
And Sovereign starts talking, in a creeeeepy voice, and calling them names like "rudimentary creatures of blood and flesh, you touch my mind, fumbling in ignorance, incapable of understanding". Yeah? Well... well, so's your mom!
So Sovereign brags for a while about how far beyond their comprehension it is. Shepard states the obvious: "Sovereign isn't just some Reaper ship Saren found. It's an actual Reaper!" Sovereign starts name-dropping, all, "Yeah, we totally killed the Protheans that one time." The general notion is that organic life is kind of an accident, and synthetic life is the pinnacle of existence. As soon as organic life becomes advanced enough, the Reapers charge in and destroy it, for reasons that Sovereign suggests are all cosmic and unknowable, but which I suspect probably boil down to "if they become strong enough, they will try to destroy us because that's what organics do to synthetics." I bet Sovereign roots for the Cylons when it watches BSG.
But Sovereign keeps dropping the plot bombs. "The Protheans were not the first. They did not create the Citadel. They did not forge the mass relays. They merely found them."
So hey, the Reapers built the mass relays for other civilizations to find, to force them to develop along the paths the Reapers desired, while they bided their time out in the dark space between galaxies. Presumably watching TV and ordering pizza from Andromeda.

Blah blah blah, "we impose order on the chaos of organic evolution", yadda yadda, "we're awesome".
Kaidan clues in to the whole "Reaper" name and realizes organic life is being harvested. Sovereign gets a little vague about what they actually want all this organic life for, then rambles about how each Reaper is a nation, "independent, free of all weakness". The
Shepard is all, "Yeah, whatever, I'll just blow you guys up." Sovereign is remarkably unfazed. "I am the vanguard of your destruction. This exchange is over." And he disappears.
Joker calls in to warn them that Sovereign - actual Sovereign, not holographic and vaguely menacing Sovereign - is heading straight for Shepard. Time to set the nuke!
More fighting with the geth, more activating and deactivating all the relevant guns and switches. They manage to take down the anti-aircraft turret. Shepard gets her team to the rendezvous point, and Joker flies the Normandy into position.

Special delivery for a Commander Shepard: one nuke, hella big.
The nuke's in position and almost ready when Ashley calls Shepard up. Apparently the geth have them pinned down in the AA tower, and the team won't make it to the rendezvous point in time for pickup by the Normandy. Kaidan points out that it'll take a few minutes to finish arming the bomb anyway, so Shepard's got time to run over and try to help. She sets off with Wrex and Garrus, leaving Kaidan to take care of the bomb.

You know, these epic race-against-time scenes are somewhat undercut by all the awkward elevator rides.
And... the geth send reinforcements over to where Kaidan's trying to set up them the bomb. Everyone strikes a dramatic pose, and Shepard asks if Kaidan can hold them off. He thinks not, and activates the bomb, to make sure it goes off no matter what. "It's done, Commander. Go get Williams, and get the hell out of here."
Aaaaaand this happens:

Ouch.
Shepard decides to rescue Kaidan. "I'm sorry, Ash. I had to make a choice." "I understand, Commander. That's the whole point of this game." (Okay, she doesn't actually say that.) So Shepard rushes back to rescue Kaidan, who's been injured and is trying to keep the geth away from the nuke. And Saren himself makes an appearance.

O HAI.
Shepard tries shooting him, but it just reflects off a super-strong barrier of some sort. Saren reveals that he's mostly helping the Reapers because he doesn't see any other choice. "The Protheans tried to fight, and they were utterly destroyed." He thinks surrender might be organic life's only hope of survival, so he's getting in on the ground floor. Shepard points out that the Reapers probably aren't gonna be big on letting them live. Saren thinks it's worth the risk, if it could mean saving trillions of lives.
He says that after he joined up with Sovereign, he created this facility to try to protect himself from indoctrination. Shepard catches the uncertainty in his posturing - "You're afraid Sovereign's influencing you. You're afraid he's controlling your thoughts." Saren shrugs it off, unconvincingly, asserting that he'd notice if it were happening.
Shep tries to get Saren to tell her about the Conduit, suggesting that they could work together to defeat Sovereign using it. He doesn't give much away. "Sovereign needs my help to find it. That is the only reason I have not been indoctrinated." Yeeeeah, Saren, buddy? That doesn't sound like a very tenable position.
Shepard keeps pushing the message that there's another option - not just submission or extinction - in the form of resistance. "I no longer believe that, Shepard." But Saren... doesn't quite sound convinced anymore. He claims he's trying to forge an alliance between organics and machines.
And then he realizes he's been monologuing for a while and decides to get on with killing Shepard to keep her from dooming their entire civilization.

Now, where were we? Oh, right, homicidal rage.
The fight does not go well for Shepard, who gets pretty beat up, but the alarm warning on the bomb starts sounding, which is all the distraction Shep needs to punch Saren in the face. He makes a run for it, and she's too blurry-eyed to shoot him as he retreats. Instead, she grabs Kaidan and retreats to the Normandy.

And the Normandy makes it out in the nick of time.
On to Part Three (in which there are lots and lots and lots of explosions)