As Unit-03 is being transported via air to Japan, a warning is delivered about a strange cumulonimbus cloud formation in its flight path. The pilot acknowledges and decides to fly through after an analysis indicates that there is no danger. However, as the Eva flies through it, a very brief but massive spark of electricity arches through the cloud.
As Shinji gets ready to go to school, he finds that Asuka has already left. Misato tells him its probably because she doesnt want to face them right now, leading Shinji to question why. Misato waves away an explanation by saying that teenage girls are hard to understand. Shinji then asks her about the things he learned from his conversation with Kensuke; namely Unit-04 and the incident at NERVs second branch and Unit-03's imminent arrival in Japan. Misato, although slightly hesitant, confirms that the rumors about the second branch's destruction are indeed true, but quickly ensures him that it won't affect NERV HQ and there is nothing to worry about. She goes on to tell him that she will be heading for Matsushiro to oversee Unit 03's activation, and that Kaji will look after him and Asuka in the meantime. Shinji takes the opportunity and asks about the identity of Unit-03's pilot, but Misato suddenly finds that she simply can't bring herself to say it, leading to a tense and awkward moment of silence between the two which is first broken when the doorbell rings. The door opens to reveal Kensuke, who desperately pleads to be chosen as the pilot for Unit-03.
Later, as Misato rides with Ritsuko in the UN convoy to Matsushiro, she admits to Ritsuko that she couldn't figure out how to tell Shinji about the pilot. Ritsuko reminds her that it was her who had to idea to volunteer to be Shinjis guardian and that knowing how to reveal the truth is her responsibility. Misato hopes that the new pilot might tell Shinji himself, but Ritsuko highly doubts that the Fourth Child would ever brag about being chosen. He wasn't enthusiastic at all when he was informed that he had been selected, and only asked for one thing: that his sister would be transferred to NERV HQ's medical center.
At school, Asuka arrives late even though she left early and when asked why by Shinji along with some teasing by a slightly distracted Toji, explodes in a fit of anger. As lunchtime comes around, Toji leaves class for the roof, something that puzzles Kensuke. His absence and odd behavior are both also noted by Shinji. Rei finds Toji, who confirms his suspicions about who knows about him. Rei admits she knows and Tojis fairly sure Asuka knows too, making Shinji the only one who doesnt know. He adds that its fairly rare for Rei to care for others like Shinji and remarks that she has feelings for him. Rei acknowledges that as probably being true. The two are seen by Hikari, who grows concerned. Toji later skips class, sitting outside, musing on his first talk with Shinji where he beat him up for haphazardly battling the third Angel.
Hikari asks to Asuka to take a walk with her after school. As they sit down a bench, Asuka guesses, correctly, that Hikari wants to talk about Toji. Hikari asks how she knew, and Asuka answers that it is pretty obvious to just about everyone that something is going on between Toji and her. That is except for Shinji, whom Asuka dismisses as too dense and inept to ever be able to pick up on such signals. Hikari then voices her concerns about Toji and Rei. Asuka reassures her, saying that someone like Rei could never get in an intimate relationship as she is the only one she considers even more dense than Shinji. She just has one question for Hikari: What exactly is it she sees in Toji? With a sight blush and a wistful smile, Hikari answers that it is his kindness. Asuka finds this hard to believe, but doesn't say it out loud.
As Asuka and Shinji sit by the TV at night, he tries to not-so-subtly probe her about the Fourth Child's identity by wondering out loud who is going to pilot Unit-03. Asuka is surprised to discover that he doesn't know yet, but even she can't bring herself to reveal the Fourths identity, and she hastily claims that she doesn't know either. Kaji then enters the living room, and immediately senses the weird tension between Asuka and Shinji; he joking asks if they are always like this when Misato is away. Asuka apologetically tells Kaji that she wishes she could be happy and smile more because he is over for a visit tonight, but she simply can't do that right now. Kaji replies that he understands, and suggests that it might be a good time for everybody to head to bed, saying that going to sleep early is often a good solution in situations like these.
As Shinji prepares to go to sleep, he asks Kaji about his father since he seems to be around him. Kaji replies that Fuyutsuki is the one who really knows Gendo the best, but even then, people can barely understand themselves so how much can they understand each other? Kaji states that this is why humans spend so much time thinking about those things and that is what makes life so interesting. "Does that mean you don't understand Misato either?" Shinji then asks him. Kaji ponders Shinji's question for a moment, and then points out that the kanji the Japanese language uses for "she" translates to "the woman far away". Kaji goes on to waxing philosophically on the subject for a bit: "To us, women will always be on the distant shore of a great gulf of misunderstanding. Basically, there's a river dividing men and women, deeper and wider than the ocean." "I don't understand adults," says Shinji after considering Kaji's words.
The next day at Matsushiro, preparations for Unit-03's action test are going smoothly as the Fourth Child is brought to the site. Misato watches on with a downcast and preoccupied expression and is barely paying attention. Ritsuko tells her to be more mindful of the task at hand, reminding her that this Eva unit will be under her command once it is activated, to which Misato half-heartedly jokes that with Evas under one's control, you could destroy the world if you wanted to. Ritsuko asks her if she has talked to Shinji about the Fourth Child yet, and Misato says she will do so once the test is over.
Meanwhile at school, Toji hasn't show up, leaving Hikari disappointed. Kensuke notes with great sadness at how Eva Unit-03s pilot must have already been chosen. He remarks that it might even be Toji since hes absent. Shinji dismisses that as being impossible, though it is obvious that he is not entirely able to convince himself of this.
In Matsushiro, phase one of the activation goes smoothly. As the procedure shifts to phase two and once the pilot goes past the absolute border line, Unit-03 starts rejecting the pilot. The unit begins to move on its own and its revealed that an Angel has infected it. This makes it the thirteenth Angel, Bardiel. Though Ritusko frantically shouts out orders for various countermeasures to contain it, the Eva breaks free of its restraints, the facility explodes.
In response to the event, NERV launches all three Eva units to deal with the situation. As Misato is currently missing in action, Commander Ikari takes personal control of the operation. As the target is revealed to be the possessed Eva Unit-03, Gendo orders the entry plug ejected, but the Angel's infection has covered the plug in a web of fungus-like strands, which keeps it stuck inside the unit. Since the pilot cannot be retrieved, Gendo changes the mission to one for which the goal is to eliminate Unit-03, reclassified now as the thirteenth Angel. Both Shinji and Asuka, however, quickly question this order, noticing that since their target is another Eva, there must still be a pilot inside it. Just then, Asuka picks up on the fact that Shinji still hasn't been told who the Fourth Child is, but just as she is about to say it, the Angel attacks and incapacitates Unit-02 in the short moment she is distracted. Rei attempts to snipe the rogue Eva, but just as she is about to take the shot, she hesitates a second too long, also noticing that there is a person inside it, leading to the Angel leaping against Unit-00 and wrestle it to the ground. The Angel then tries to infect Unit-00 too by dripping its fungus-like material on its opponent's arm, but Gendo orders the Eva's arm blown off. The resulting shock from the pain leaves Rei utterly unable to fight, and so Shinji is the only one left to face the Angel.
Staring down Unit-03, Shinji hesitates to move against it, as he considers that that might be a person in it, another child about his own age. Unit-03 takes advantage of his hesitation, and makes a leap against him and manages to knock Unit-01's weapon out of its hands and the Eva to the ground. Shinji now sees Unit-03's entry plug, confirming to him that there is a person inside it. Shinji barely manages get his Eva back on its feet, before the Angel's arms suddenly jump forward, and grasps Unit-01's neck, and starts choking the life out of both the Eva and Shinji. Yet, Shinji does not actively resist. Gendo asks him over the radio why he refuses to fight, telling him that the life of Unit-03's pilot is "irrelevant." Shinji responds that he refuses to risk killing the person in Unit 03, and would rather die himself than allow that to happen. In a complete matter-of-fact manner, Gendo orders Shinjis connections cut off and the control transferred over to the dummy plug. Ibuki is hesitant, saying the dummy system is still buggy, but proceeds to follow Gendos order.
Shinji sits back in utter surprise as his control over Unit-01 is suddenly relinquished and the pressure on his neck disappears. As the dummy system assumes control over Unit-01, the Eva immediately goes on the offensive and soon gains the upper hand over Unit-03, and it proceeds to annihilate the Angel in the most brutal fashion imaginable. After choking it and breaking its neck, the dummy system throws Unit-03 down, pulverizes its face, and proceeds to rip apart and mutilate Unit-03 as all the NERV personnel watch in horror. Shinji, forced to see and hear everything, repeatedly begs his father to stop even as Unit-01 lifts up Unit-03's entry plug in its hands but Gendo simply watches with grim satisfaction as Unit-01 crushes the entry plug. A stunned silence falls over Central Dogma. "Eva Unit-03, no, I mean, uh... the target is completely silent," declares Aoba hesitantly.
Later that night, Misato comes to as the rescue team lifts her out of the remains of the Matsushiro facility. Kaji is at the scene, and he tells her that she and Ritsuko are among a handful of survivors, and about what happened to Unit-03. She calls Shinji, who still sits in the powered-down Unit-01, to try and reveal the pilots identity but still cant bring herself to say it as she starts to break down sobbing. As Shinji watches the team pull out a broken but alive Toji from the wreckage, he begins to scream.
- Armor-Piercing Question: A downplayed example. Kaji talks to Shinji about how people find it very difficult to understand both each other and themselves, and so spend a lot of their time trying to figure those things out, then and adds that, from his point of view, the time spend contemplating these subjects is what makes life truly interesting. Shinji considers his words, and then asks if him is that also true for him and Misato. Kaji is visibly surprised at the question (and, it is implied, at Shinji being much more perceptive of other people than he thought), and talks a brief moment to formulate a somewhat vague and more general response about the nature of men and women.
- Color-Coded Characters: Toji's unit has the same colors that he wears to school: Dark purple/black with white and light purple.
- Dramatic Irony: Pretty much everyone, both the main characters and the audience, knows perfectly well that Toji is the Fourth Child. Shinji, however, remains firmly Locked Out of the Loop until the very end, and it is Played for Drama as much as possible.
- His Name Is...: Asuka is just about to reveal on the battlefield to Shinji that Toji is the Fourth Child, but she is knocked out cold by Unit-03 just before she can actually say his name.
- Meaningful Look: When Asuka is fuming in anger upon her arrival in class, she shouts at Shinji, Kensuke and Toji, but have her eyes fixed in a subtle Death Glare at Toji the entire time, as she knows that he is the Fourth Child and is rather displeased with that fact.
- No Good Deed Goes Unpunished: A very immediate version. When Asuka realizes that Shinji is still Locked Out of the Loop about Toji being the pilot of Unit-03, she finally decides to do the thing everyone else, including herself, have been avoiding up to his point, namely telling him the truth. Unfortunately, she does in the middle of battle and the distraction leads to her getting knocked down before she can tell Shinji.
- Oh, Crap!: When Bardiel in Unit 03 rounds a mountain on its way to Tokyo-3, pretty much everyone in the NERV control room has this reaction.
- Sweat Drop: Utilized by Asuka when Hikari explains her attraction to Toji.
- Wham Episode: Though the show had been getting increasingly darker by this point, this episode signals the onset of full-on Cerebus Syndrome.
- What Does She See in Him?: Asuka asks Hikari this exact question about Toji.