It is 22 days before now, and NERV is holding an activation test with Rei for Unit-00. Gendo, sporting a different pair of glasses, orders them to begin the test. The first part of the activation runs along smoothly, but at the critical point before the synch rate reaches the activation minimum, something goes wrong. Unit-00 begins struggling against its restraints, breaks loose and begins pounding at the safety glass to the observation room, breaking it and almost injuring Gendo. Rei's entry plug is rejected and flails around the room, before landing hard on the floor of the test chamber. In an attempt to stop the Eva, Ritsuko orders it sprayed with Bakelite to restrain its movements. Finally the Eva's battery runs out, and in the same instant, Gendo storms towards the entrance of the test chamber. He heads straight for the entry plug, and despite badly burning his hands, he forces it open manually. He is relieved to see that Rei is still alive and conscious. Meanwhile his glasses, which he dropped on the floor, crumbles and breaks from the heat.
Later, Unit-00 is in the process of being freed from the Bakelite. Ritsuko explains to Misato that its pilot is Rei, who is "the first child selected by the Marduk Report", and that "her past has been eradicated, all her personal records erased." Misato asks what went wrong with the test, and Ritsuko says that it isn't completely clear, but they "believe that mental instability on the part of the pilot was a primary cause." Misato starts questioning this explanation, and Ritsuko begins to doubt it for a second too, but she snaps out of it and mumbles "It can't be that."
In the present, at the site where Shinji killed the latest Angel, NERV is out in force to examine its almost intact corpse and have managed to partly recover the Angel's damaged power source. An excited Ritsuko shares her findings with Misato and Shinji: The computers cannot fully analyse the matter the Angel is composed of, but it has an "inherent wave pattern" making it a "form of matter similar to light" and it shares a 99.89% likeness with human DNA. Shinji, meanwhile, sees that Gendo and Fuyutsuki is out to inspect the findings. Looking at them from a distance, he sees that his father has taken his gloves off, and that his hands has burns on them. Misato notices his curiosity, and Shinji asks her about his father's wounds. Ritsuko tells him that he suffered them while he saved Rei from an accident with the Eva. This catches Shinji's interest as it conflicts with the view he has of Gendo and he starts to wonder what kind of connection he has to Rei.
In school, Shinji watches Rei as the girls go swimming in physical education, still puzzled by her. Toji and Kensuke notices it, and teases him for peeping at Rei, asking him if he is interested in her. Shinji begrudgingly admits that they are right, but tells them that it is not in the way they think; he is more curious about why she is always alone. Both boys admit that they know next to nothing about Rei, as she is always quiet in class, and no one really wants to socialize with her as she has something "unapproachable" about her. Kensuke asks Shinji if he shouldn't know more than them, since he is an Eva pilot like her. He admits that he hasn't really spoken to her.
Same day, at a synch test, Shinji watches Rei through the Unit-01's camera. He notices that Gendo walks up to her, and zooms closer in. He is shocked to see that they are both smiling, and are apparently having a pleasant conversation.
Same night at Misato's apartment, Ritsuko is invited over for dinner. As it is Misato's turn to cook, she insists on serving her own mixes of various TV dinners, much to Shinji and Ritsuko (and Pen Pen)'s displeasure. During dinner, Ritsuko asks Shinji to do her a favor: Rei has been issued a new access card, and she wants him to deliver it. Seeing Shinji looking intensely at Rei's picture on the card, Misato decides to tease him over his interest. Embarrassed, Shinji explains that he just finds Rei strange because he knows so little about her. Ristuko tells him that Rei is a nice girl, but she is a bit like Gendo, "not very adept... at living."
The next day, Shinji goes to Rei's apartment, which lies in an almost abandoned tenement in an older part of the city. Finding that the doorbell does not work, and the door is unlocked, he ventures inside, calling for Rei, but gets no answer. He notices that Rei's apartment is quite dirty and dusty, and has medical supplies and bloodstained bandages lying around on the furniture. He spots a pair of damaged glasses on a commode (unbeknownst to him it is Gendo's old glasses) and he picks them up.
Suddenly Rei steps out of her bathroom, having showered. She sees that Shinji is holding the glasses, and, apparently oblivious of her nakedness, heads straight for him, with her hand reaching for the glasses. Shinji panics, and with his bag strap caught on the underwear drawer he trips forward, emptying its content over the floor. Having landed on top of Rei, Shinji freezes completely up. Finally, after a long moment of intense awkwardness, Rei coldly asks him to move, and he notices that he is accidentally groping her, and he quickly jumps back.
Not further acknowledging his existence, Rei carefully stores the glasses in their case, and starts to get dressed, while a flustered Shinji tries to explain himself, but she leaves before he can hand her the new access card. He follows her as she heads for NERV HQ, but she seemingly pays him no mind. At the access gate, Shinji finally gets to hand Rei the card, but she continues onward with no comment. Shinji tries to strike up a conversation with her, and apologizes for what happened in the apartment, but Rei apparently doesn't know what he wants to apologize for. Changing the subject, he asks her if she isn't scared about the upcoming activation test for Unit-00 when she was so badly hurt the last time. She asks him if he has faith in his father's work and Shinji flat out tells her that he doesn't trust Gendo. It apparently strikes a cord in the stoic girl, as she, without a word, turns around and gives him a glare before slapping him. She then goes back to ignoring the surprised Shinji.
The second activation test for Unit-00 commences. This time the activation minimum is passed without problems and Unit-00 is deemed operational. Just as the test is completed, NERV is contacted about an approaching object, a huge, floating crystalline octahedron that is most likely the Fifth Angel, and goes into alert. Gendo opts to use Unit-01, as he believes that Unit-00 isn't fit for battle yet. Rei breaths a sigh of relief as the test is over.
Unit-01 is launched against the Angel, but on its way to the surface, Hyuga picks something up on the scanner: The Angel is rapidly accumulating energy. Misato frantically shouts a warning to Shinji, but it is too late; Unit-01 have barely arrived on ground level before it is struck by a beam of concentrated energy that hits it square on the chest. Shinji screams out in extreme agony.
- Berserk Button: Gendou is this to Rei. Her reaction to Shinji with his glasses is to try and attack him, and when he says that he can't have faith in him Rei slaps Shinji. He's just as shocked as the viewer, and this would be addressed as the series goes on where Rei would gradually subvert and then avert her feelings towards Gendou entirely.
- Cliffhanger: The last of its kind in the show, and, boy, are the stakes ever raised higher with the episode ending on Shinji getting shot by a high-powered laser?
- OOC Is Serious Business: The unheard conversation between Gendo and Rei is really quite unique as Gendo's demeanor actually somewhat resembles that of a proud father for once, while Rei is positively bubbly. Shinji's surprise pretty much mirrors the audience's.
- Elaborated on further when she catches Shinji with his father's glasses. She tries to take them off him and attack him upon seeing this, and attacks him again when Shinji badmouths his father. According to the manga Gendou is the only person Rei has faith in, and he is something of a Berserk Button to her.