Starting where the previous episode left off, Shinji, inside Unit-01, faces the attacking Angel in the streets of Tokyo-3. Unsure of what to do, he is told that the Eva will perform the actions he thinks of, and he should therefore start off simple with concentrating on walking. He manages to take one feeble, yet successful, step before losing his balance, making the Eva trip and land on ground, face first. Before he can manage to get Unit-01 on its feet, the Angel advances on them. Frozen with fear, he fails to resist as the creature picks the Eva up by the face and breaks the arm of the Eva. This somehow transfers the same immense pain to Shinji's own arm, and he instantly panics. The Angel then starts pounding on the Eva's skull, and once again Shinji feels the pain of every single blow. After a series of attacks, Unit-01's skull carves in, and the Angel's attack penetrates its brain, causing a massive blood loss. Shinji looses consciousness, all readings on him goes blank, and a panicked Misato calls out his name.
Shinji then awakens in a hospital bed. Getting his senses together, and examining his surroundings, he notes that he is looking at an "unfamiliar ceiling."
Meanwhile, in the center of Tokyo-3, a NERV operation headed by Misato and Ritsuko is in the process of cleaning up after yesterday's battle. And Misato notices that the government has already gotten the media to cover up the event. As this goes on, Gendo is having a holographic meeting with the benefactors of NERV, the Human Instrumentality Committee, a group under the United Nations headed by Chairman Keel Lorenz. They discuss the reappearance of the Angels after the 15 years since Second Impact, and expresses their concerns toward the costs of the operation and the publicity it is getting. Keel interjects that the appearance of the Angels is no excuse for letting the Human Instrumentality Project fall behind schedule, and Gendo ensures the committee that it will not happen. As the meeting comes to an end and the other committee members are logging off, Keel privately tells Gendo that "there can be no turning back", before signing off himself. "I know," says Gendo ominously, "Mankind has no time left."
Meanwhile at the hospital is Shinji is wandering around in a daze, confused about the previous day's events. Another patient is wheeled past him, and he notices that it is Rei, who stares blankly back at him, before she disappears down the corridor. Risuko gets a phone call about Shinji's awakening. Misato asks about his well-being, and while she is ensured that he is physically healthy, she is still cornered about what impact the last day will have on his psyche. As Risuko is letting Misato out of her car, the latter states that they might actually stand a chance against the Angels. "You're always such an optimist," says Ritsuko. "Your attitude does make me feel a little more at ease..."
Much to Shinji's surprise it is Misato who picks him up at hospital. On their way out, they encounter Gendo, and Shinji adverts himself from his gaze. After a prolonged period of unconformable silence, Gendo leaves. In a voice-over, Risuko asks Fuyutsuki why Shinji and Gendo doesn't live together. "I think that living apart is natural for Ikari and his son," replies Fuyutsuki with a hint of sadness. A puzzled Risuko then asks why them being together would be unnatural.
Misato then finds out that Shinji is going to live alone in an apartment complex inside the Geofront. She asks him if he is okay with that, and he says that he is perfectly fine with it, since he is "alone anyway."
In a phone call, Misato tells a surprised Ritsuko that she is taking Shinji in to live with her, and ensures her that she "isn't going put the moves on him." Risuko angrily chews her out for even joking about it being a possibility. On the way back to her apartment, Misato takes Shinji to an overlook spot, and shows him the sunset over Tokyo 3, the city he helped save.
Standing outside the apartment door, Shinji is reluctant to step over the doorstep, not wishing to intrude on Misato's hospitality, but encouraged by her, he takes the step and hesitantly declares "I- I'm home." She responses with a cheerful "Welcome home!"
Shinji now sees what sorry state Misato's apartment is in, with beer cans, trash bags, and half-eaten food lying around everywhere. Meanwhile Misato opens a beer and completely drops her professional attitude, and one moment berates Shinji for his withdrawn attitude and the next telling him that he just fine the way he is, only adding to his confusion. After he has repeatedly lost a quick rock-sissors-paper tournament to distribute the house chores, Misato suggests Shinji to take a bath for him to relax a bit. Inside the bathroom, after taking his clothes off, he is surprised by a penguin, causing him to panic and run into the kitchen completely naked, while babbling incoherently about the thing he saw in the bathroom. As the penguin casually waddles past him, Misato nonchalantly introduces him as Pen Pen, the third occupant of the apartment. As Shinji's dumbfounded glance follows Pen Pen around the room, Misato, just as nonchalant as before, tells him that he should really consider putting on some pants. It takes him a moment to realize he isn't wearing any clothes, and he quickly retreats embarrassed to the bathroom. "Maybe I'm being overly flamboyant... He might be able to see right through me," mumbles Misato to herself once she is alone.
In the bath, Shinji contemplates the events of the past two days. He admits that he kind of likes Misato and wonders about the nature of Rei, remembering her mysterious appearance in the middle of the street, and what her connection to his father is.
Meanwhile, inside the Geofront, Gendo and Ritsuko is overlooking the frozen down Unit-00, and she ask him if him visited Rei at the hospital; "They say she'll be ready to work in twenty days," replies Gendo. "It's so hard on these poor children," laments Ritsuko, but Gendo curtly replies that they are the only ones that can pilot the Evas and he will continue to make them do so.
While Misato is taking a bath, Shinji new lies in his new bedroom listing to his SDAT player, and the events of the night before suddenly comes back to him.
Despite its massive head wound, the heavily injured Unit-01 suddenly starts to move by its own power again. A scared Risuko gasps that "It's gone berserk..." The Eva, roaring like a wild beast, starts relentlessly attacking the Angel while Gendo and Fuyutsuki exchanges knowingly glances, the latter declaring "It looks like we've won." The Angel attempts to fend off its attacker by putting up its A.T. Field, but the Eva counters by healing its own broken arm and ripping apart the energy barrier. The Eva then straddles the Angel, and starts savagely pummelling the creatures core, causing it to crack. In a last ditch effort the Angel wraps itself around Unit-01 and self-destructs in a huge explosion, but the Eva takes no damage from this. Having re-established contact to the cockpit, Shinji is confirmed to be alive and conscious. Looking around in a state of shock and disbelief, he notices the reflection of Unit-01 in a nearby building. The Eva's heavily damaged helmet then slides off, and reveals the injured head underneath. The face of Eva then spontaneously regenerates in front of Shinji's eyes, and a big green eye looks back at him. The sight makes him scream in terror.
Back in the present, Misato stands in the doorway into Shinji's bedroom and tells him that he did good today, and that he has reason to feel proud of himself, telling him to "...Hang in there" before leaving.
* AllThereInTheScript: The members of the Human Instrumentality Committee are from different nations, and are as follows: Keel (Germany), Yellow member (France), Blue member (Russia), Green member (USA), Red member (UK).
* HowWeGotHere: Set up early in the episode, though the actual "how" is first shown near the end.
* UnfamiliarCeiling: TropeNamer.