With such a promising title, The Beginning of the End begins to mash up characters that haven't seen one another for half the season. Sophia does another mood swing and actually starts to feel sympathy for the poor humans she's about to exterminate. Jarvis gets some bad news, and Sterling and Simon become the new super-team we can cheer for. All they need is someone with super computer hacking powers...hey, wait a minute!
As the penultimate episode, the show teases a few more reveals about the aliens. But of course those have to wait until next week, if at all, given The Event has been cancelled. But even without that dark cloud hanging over it, there's little to get excited about anymore, and few characters left to invest in aside from Sterling and Simon. It's notable that the virus in question could have killed most of humanity in just half the time that this plot has been dragging over the last few weeks.
All this talk of genocide manages to give Sophia a nightmare—she's walking through a town full of dead people and gets screamed at by a little girl. She wakens to get news from Dr. Liu that Leila's body has mutated the strain into a slower-acting virus, a virus that will kill most of the human population (also the virus is now bitchy and super annoying, too). Sophia is suddenly reluctant, given she only want to kill a couple of billion. Did the evil alien queen find her conscience?
Carlos lets Sophia know that they're nearly ready for all their people to come through. Time is running out on their homeworld. But they do need to move a surveillance satellite that can track the portal in Tibet, so Sophia puts a call into VP Minion. He has some news too—Martinez is improving. Jarvis wants her word she'll spare the American people if he does what she says. She swears. Liar!
Simon fills Sterling in on Sophia's mission to Siberia looking for a weapon, but he doesn't know what she might be searching for. Peel's already advised Sterling about Jarvis letting the passenger plane land. On the television, Simon conveniently recognizes the face of one of his people—the guy Vicky shot—as the news is about the terrorist attack at the mall.
Meanwhile, Sean's still upset with Vicky for letting Alexandra get away. They find an address in the wallet and arrive at some distribution warehouse. As they go searching around, Vicky gets caught—by Simon! Sterling comes out and gets a gun in his back from Sean. They have a brief standoff. Then everyone recognizes everyone and Sterling's like "Sean Walker from the plane?" And Vicky's like "Blake Sterling of the NSA?" And Sean's like "Simon, the alien?" Calmer heads prevail and they join forces to form a new super team to go through the building and see if they can find anything to locate Sophia's new base of operations.
Sterling recognizes Vicky as former CIA. She's all "I don't know what you're talking about." And that's all anyone says about that again. Sean asks if Simon thinks Leila's still alive. Maybe, but Michael's toast, he says. Seans says he'll find her when this is all done. Then the sound of a garbage truck alerts them to the fact that the agent could have tossed stuff before he left, so they start going through the bin, finding addresses and all sorts of goodies.
At the hospital, Jarvis gets informed of Martinez's improving condition. The doctors can't explain it. The First Lady comes up and gives him a whack across the face and makes a huge scene in the hospital. Then they announce the president is awake.
It's a miracle! The First Lady brings him up to speed on what he missed and Jarvis' deception. Then Sterling gets a call from Martinez and he gets all sappy. Sterling also brings him up to speed, so Martinez says he'll deal with Jarvis and wants to return to the White House immediately.
Sophia has agents everywhere, apparently, as they manage to start distributing the virus at the airport and the treasury. She does ask about Leila's condition, and it's unclear how long she'll fight off the virus. Sophia sees she's suffering and tells Dr. Liu to end it painlessly.
Sean gets Sterling into his NSA account to search the route of the alien agent—somehow using satellites. They track his car to a building that's seen a lot of activity so they all head there. En route, Simon notices Sean's scrolls he got from Dempsey that he just happens to be carrying around, and asks what he knows about it. Dempsey must have known more than he was letting on if he could read those, Simon says cryptically. And that's all we hear of that, too, because Sean doesn't ask what he meant.
The four of them take out the guards at the entrance and head inside, just as Dr. Liu starts injecting Leila to put her to sleep before giving her the final shot to kill her. But Leila isn't as sick as she's letting on and breaks free of her bonds and injects Liu with the needle. Conveniently enough, that's when Sean arrives, but Leila's sealed inside her virus room and lets him know that the strain is going to be released soon. Leila tells him she's infected, and Sean's all "Huh?"
Martinez arrives at the Oval Office and tells Jarvis to get the hell out. But Jarvis says he's the president and everything he's done has been for America. Oh, and Martinez did have a stroke, for Pete's sake, so it's likely he won't be certified capable of resuming his office if Jarvis has anything to say about it.
Next comes suffering through Sean and Leila's long good-bye while Sterling and Simon look through Liu's computer for an antidote. Liu is revived so Simon can try to torture her to get her password. She gives it up pretty fast after he puts a drill to her head, but it's too late, she tells him. All they see are distribution figures and no way to figure them out in time. Meanwhile, the satellite is diverted and the array begins to power up.
Next week—the event?