Sophia is starting to have second thoughts about killing 98% of all the humans on the planet. But this doesn't stop her from going ahead with the plan, which involves spreading the virus in three different ways. For some reason, the three places she plans to infect are "The Eastern Seaboard," "The Entire United States," and "The Entire Rest of the World." It seems like if you need only one virus-spot to infect the entire world, it's kind of a waste to devote another spot to just infecting a relatively small portion of one country.
Vicky and Sean actually meet up with Simon and Sterling, and aside from some early gun-waving, everyone seems to get along pretty well. They hack into an NSA satellite archive and track Beardo back to the Alien Garage, but by the time they get there, almost everyone's gone. They do find Leila, who's dying of the superflu, and she and Sean have a pretty good scene where she tells him that she has to stay in the clean room or he'll die. Meanwhile, the professional spies are threatening the nefarious Doctor Lu so they can get her laptop password. They don't know what the alien plans are, but they know they're on the laptop somewhere, so that's something of a cliffhanger.
And in Vengeful President news, Martinez has basically recovered. In fact, he's so recovered that he's able to walk back into the Oval Office (on canes) and threaten Jarvis. Jarvis says Martinez can't be president again until the cabinet says so, and they might be a little leery about doing that what with the multiple strokes. This affects the alien plot, because Jarvis is having the NSA make a satellite look away while Sophia portals her billions of people over. So that, too, is a cliffhanger.
Oh, and apparently the aliens were here before humanity. And that super-old scroll that Hal Holbrook gave Sean is proof of that. So that'll be an interesting thing that never gets paid off, right? I mean, we're all agreed that next week's season finale is going to end with a monster cliffhanger that will never, ever get resolved?
Sophia walks through a city square that's full of dead people and crashed cars. I can't swear to this but, I think it's the city square location that was used in Back to the Future. Oh, except that that burned down in the Universal Studios fire. I'm off to a bad start here. Just like the episode! Damn, I just think I burned this show so hard, it got cancelled. Sophia wanders around and calls out, "Hello?" a lot. This is clearly a dream sequence, because if it were real, that would imply that something had actually happened. I find it annoying that this was in the "Next Week" thing last week, because I think it's cheating. Sophia eventually finds a car with a bloody zombie-looking girl in it. She's not really a zombie; I've just been programmed by popular culture to always think someone's a zombie when they're covered in pancake makeup and stage blood. The girl's contribution to this scene is to beg for help and ask if Sophia's the doctor. She isn't. The girl's mother told her to wait there until she got back. She asks, in a generically plaintive tone, why her sick brother won't wake up. Kid, open your eyes. There are like twenty dead bodies in clear view of your car. I know death is confusing, but you should have figured out the concept at some point during the apocalypse which apparently befell this picturesque city square. She starts shouting "It's your fault!" at Sophia.
Sophia wakes up, of course. Maybe she had a bad dream because she was sleeping on one of those cots. Most of the other cots are empty, so I think she's sleeping in the middle of the day. And now that she's awake, it's time to check in on the Genocide Plan. Doctor Lu reports that injecting their special Spanish Flu virus into Leila caused it to mutate in exactly the way they wanted. So it's still very deadly, but it takes a little bit longer, allowing it to be transmitted before the host dies. Now, the virus changed dramatically when they injected into Leila, because she's only half-human. Doesn't that mean it's going to change again when they take the version from Leila and reinfect humans with it? Oh, never mind. I'm sure the alien doctor is a supergenius who can exactly predict how viruses mutate. And sidelines as an acupuncturist. The official word is that this flu will kill 25% of the human population after two weeks and 98% after five weeks. Sophia thinks that's too many, because she only wants to kill enough humans to make room for her people. Well, if everyone's okay sleeping in cots laid out in a warehouse like this, you need a lot less room than I thought. But she doesn't object strongly enough to change the plan or anything. She's willing to say "This goes against everything we believe in," but she's still approving it.