The episode starts where the previous one ended: Shinji, inside Unit-01, faces the attacking Angel in the streets of Tokyo-3. Ritsuko tells Shinji that the EVA will perform the actions he thinks of, so he should start off with the simple act of walking. He manages to take a feeble, yet successful, first step -- but when he goes for another, he loses his balance. Unit-01 trips and lands face-first; before Shinji can get the EVA on its feet, the Angel advances. Frozen with fear, Shinji fails to resist as the creature picks Unit-01 up by the head and breaks its left arm. This act somehow transfers an immense pain to Shinji's own arm, and he panics as a result. The Angel starts pounding on the EVA's head with a unique energy attack; Shinji again feels the pain of every single blow. The Angel's attack eventually penetrates the EVA's casing and sends it reeling backwards, the biomechanical being losing blood at a significant rate. Shinji loses consciousness, all readings on him go blank, and a panicked Misato calls out his name.
Shinji awakens with a start in a hospital bed. After getting his senses together and examining his surroundings, he lies back down and notes that he's looking at an "unfamiliar ceiling".
In Tokyo-3, a NERV operation headed by Misato and Ritsuko cleans up the city and recovers the EVA after the prior day's battle. Misato notices how the government has already gotten the media to cover up the event. While the cleanup and "sanitation" occurs, Gendou holds a holographic meeting with NERV's benefactors: the Human Instrumentality Committee, a somewhat clandestine group headed by a Chairman Keel Lorenz, operating under the United Nations. The whole group discusses the reappearance of the Angels fifteen years after Second Impact and expresses their concerns toward the economic costs of the operation (as well as its publicity). Keel rebukes the appearance of the Angels as an excuse for letting the Human Instrumentality Project fall behind schedule, and orders Gendou to treat it as his highest priority. The Committee excuses Gendou from the rest of the meeting so it can privately consider NERV's appeal for more funding, but Keel takes a moment to let Gendou know "there can be no turning back", to which Gendou replies that he knows mankind has no time left.
At the hospital, Shinji wanders around in a daze, confused about the previous day's events. Another patient is wheeled past him; he notices that it is Rei, who stares blankly back at him, before she disappears down the corridor. As Misato and Ritsuko drive back to the Geofront, the latter gets a phone call about Shinji's awakening. Misato asks about his well-being; while she receives assurance about Shinji's physical health, she worries about what impact the last day will have on his psyche. As Ritsuko drops Misato off, the latter says that humanity might 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."
Misato picks up Shinji at the hospital, but on their way out, they encounter Gendou. Shinji adverts himself from his father's gaze, and after a prolonged period of uncomfortable silence, Gendou leaves. In a voice-over, Ritsuko asks Fuyutsuki why Shinji and Gendou don't live together. "I think that living apart is natural for Ikari and his son," Fuyutsuki replies, a hint of sadness in his voice. A puzzled Ritsuko asks why them being together would be unnatural.
After leaving the hospital, Misato finds out Shinji plans to live alone in an apartment complex inside the Geofront. She asks Shinji if he's okay with that, and he says he has no problem since he already feels alone. Moments later, Ritsuko gets a phone call from Misato: Shinji will instead move into Misato's apartment. Misato says she won't put any moves on Shinji, and Ritsuko chews her out for even joking about that being a possibility. On the drive 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 hesitates to step over the doorstep, not wishing to intrude on Misato's hospitality, but after Misato encourages him, he takes the step and hesitantly declares, "I-I'm home." She responds with a cheerful declaration: "Welcome home!"
Only after the welcome does Shinji see the sorry state of Misato's apartment: beer cans, trash bags, and half-eaten food sits on nearly every flat surface. He opens the refrigerator to find TV dinners and beer. Shinji, concerned about the lifestyle Misato seems to lead, wonders what he has gotten himself into. He notices another, larger refrigerator, and asks Misato about it -- but her absent-minded answer ("Ah, don't mind that. He's probably still sleeping.") doesn't really answer Shinji's query.
As the two of them sit down for what amounts to dinner in her home, Misato opens a beer and completely drops her professional attitude. She berates Shinji for his withdrawn attitude, then tells him that he's fine the way he is, which only furthers the boy's confusion. After distributing house chores via rock-paper-scissors (with Shinji losing more than winning), Misato suggests Shinji should take a bath to relax a bit. Inside the bathroom, Shinji is surprised by a penguin...which causes him to panic, run into the kitchen completely naked, and babble about the thing he saw in the bathroom. As the penguin waddles past Shinji, Misato introduces the creature as Pen-Pen, the third occupant of the apartment. Shinji can only stand dumbfounded as he watches Pen-Pen move through the room and enter the large refrigerator, which looks like a miniature apartment on the inside. Misato turns back to Shinji and tells him that he should really consider putting on some pants. When Shinji realizes he doesn't have any clothes on, he blushes all over and retreats to the bathroom. This prompts Misato to wonder if she's acting too flamboyant.
In the bath, Shinji contemplates the events of the past two days. He admits that he (kind of) likes Misato, then wonders about the nature of Rei (considering her mysterious appearance in the middle of the street) and her connection to his father.
Inside the Geofront, Gendou and Ritsuko overlook the frozen Unit-00. Ritsuko asks Gendou if he visited Rei at the hospital; Gendou only says Rei can go back to work in twenty days. "It's so hard on these poor children," laments Ritsuko, but Gendo reminds her that only those children can pilot the [=EVAs=] -- and he will continue to make them do it.
Misato takes some time to talk with Ritsuko over the phone while taking a bath. She tells Ritsuko about Shinji's attitude and demeanor, then expresses doubt to whether he might pilot Unit-01 again, so Ritsuko says Misato -- now Shinji's new guardian -- must help maintain Shinji's mental stability. When Misato admits to feeling overwhelmed by that task, Ritsuko jokes about Misato making the decision to take Shinji home. Misato hangs up on Ritsuko, then thinks about how she only saw Shinji as a tool to defeat the Angels a day prior and wonders if that makes her the same as Ritsuko (a thought that makes her unhappy).
Shinji lies in his new bedroom, looking at yet another unfamiliar ceiling, while listing to his SDAT player. The events of the night before slowly comes back to him...
The Angel's energy attack eventually penetrates the EVA's casing and sends it reeling backwards, the biomechanical being losing blood at a significant rate. Shinji loses consciousness, all readings on him go blank, and a panicked Misato calls out his name. Despite the massive head wound, the EVA starts to move again ("It's gone berserk," claims Ritsuko). Unit-01 roars like a wild beast, then charges at the Angel without hesitation. Gendou and Fuyutsuki exchanges knowingly glances, and the latter declares victory over the Angel. The creature attempts to fend off the EVA by putting up its A.T. Field as a wall, but Unit-01 counters by healing its own broken arm and ripping the energy barrier apart. More attacks put the Angel down on the ground, at which point the EVA straddles the Angel and pummels the creature's core until it cracks. Sensing its own defeat, the Angel wraps itself around Unit-01 and self-destructs; this act causes a massive explosion...but Unit-01 survives with no extra damage.
When NERV re-establishes contact to the cockpit, they confirm Shinji as both alive and conscious. He looks around in a state of shock and disbelief -- and notices the reflection of Unit-01 in a nearby building. The EVA's damaged helmet slides off and reveals the injured head underneath. Unit-01's face spontaneously regenerates in front of Shinji's eyes, and a large green eye looks back at him. The sight makes him scream in terror.
Shinji's flashback ends when Misato knocks on his door. She stands in the open doorway and assures him that he has a good reason to feel proud of himself, telling him to "hang in there" before leaving him to rest.
!! ''Episode 02: Unfamiliar Ceiling[=/=]The Beast'' contains examples of the following tropes:
* AllThereInTheScript: The members of the Human Instrumentality Committee all reside in different nations: France (yellow member), Germany (Keel), Russia (blue member), the United Kingdom (red member), and the United States (green member).
* HowWeGotHere: The episode sets this up early on, but doesn't show the actual "how" until near the end.
* MirrorScare: Unit-01's reflection in the building, a hint at its EldritchAbomination visage, is enough for Shinji to pull off a ScreamDiscretionShot.
* SceneryCensor: As Shinji runs into the kitchen naked after being surprised by Pen-Pen in the bathroom, his "naughty bits" are hidden by a beer can on the table in the foreground. During the conversation that ensues, Misato picks up the can, revealing that Shinji's modesty is still defended — by a much smaller container clearly labeled "toothpicks".
* UnfamiliarCeiling: This episode is the TropeNamer.