After the incident involving Leliel, Misato is interrogated by the Human Instrumentality Committee. Keel opens the round of questioning by asking about her continued refusal to let Shinji, the most direct witness to the incident, testify before the committee; Misato defends her decision, citing that Shinji that is "too unstable, emotionally speaking" to participate in an official debriefing. The other committee members then join in with questions of their own, asking her about what exactly the Angel intended to do with Shinji after it pulled him into its body and they are curious about whether it made contact with his mind. Misato essentially says that there is no hard evidence to support that idea and that trying to understand what the Angel meant to do is impossible. As to whether something like this will happen again in future, Misato answers that since there has been no organization or teamwork among Angels, what happens with one Angel does not provide any clues as to what will happen with future Angels. As the interrogation concludes, Misato is dismissed and the Committee turns to Gendo, asking him about his thoughts. "The Angels are beginning to attain intelligence," Gendo states. "The time left to us is...", "Running short?" says Keel as he finishes Gendo's sentence.
Toji steps out of an elevator; he is visiting his sister in the hospital. The nurses talk about him amongst themselves, noticing he shows up two times every week, without fail. They admire him for his loyalty to his family: "He has a good heart." Meanwhile, in NERV HQ, Gendo asks Rei if she is feeling all right. Rei responds dutifully she is fine and she will see Ritsuko tomorrow and then return to school the day after that. Gendo then asks her how she is doing in school, and he is pleased hear that she has no problems. In Shinji's class, the class teacher is reading the names of the currently absent students, listing among others Rei and Kensuke. Noticing this, Shinji asks Toji why Kensuke isn't in class; "New Yokosuka. Chasin' battleships again today," answers Toji somewhat absent-minded while staring out the window. Toji is then called to attention by the teacher, who asks him to give Rei the printouts of her missed school work after class.
In NERV Headquarters, urgent news comes in from Nevada where the second branch of NERV's American department is located. During the SEngine activation test for Eva Unit-04, there was an error of some sort that caused the second branch and everything else in an 89 km radius to disappear completely, including several thousand people working at the second branch. It was not just an explosion, however. Ritsuko states that they were most probably swallowed by a Dirac Sea similar to the one Unit-01 was sucked into. Misato asks what happened to the Sengine itself, and Ritsuko tells her that it has vanished too, along with their chances to elevate their understanding of its inner workings. "That's what we get for trying to push ourselves into using something we don't understand," replies Misato, but Ritsuko notices privately that that also applies to the Evangelions. The U.S. government, which was in charge of developing Units 03 and 04, deems that having the surviving Unit-03 contained in the first branch is too dangerous in the wake of the disaster, and orders it shipped to Japan. When Misato asks whether Reis dummy plug will be used in the activation test, Ritsuko answers that she still has to decide that.
Later that day, Gendo has a look at Reis dummy plug. Reis thought patterns, which have been recorded many times over in the tank of LCL in Central Dogma, are being used to trick the Eva into thinking that there is an actual pilot inside of it. Ritsuko states that with current technology, however, it is still impossible to completely digitize a human mind and soul and that the dummy plug is just a crude imitation. Gendo orders the plug to be loaded into Units 01 and 02, even after Ritsuko warns that there are still many bugs that have not been taken care of. Gendo later moves into Central Dogma and watches Rei as she sits in the LCL tank. He orders Ritsuko to take care of the activation of Unit-03 at Matsushiro at the end of the week. She says that with the risks of the dummy plug, activation will be handled with the Fourth Child. He fails to notice Ritsuko watching him with a sullen expression on her face as he invites Rei to eat together.
In the classroom, a happy Toji excitedly looks forward to his lunch, calling it "the single best thing about school!" As he prepares to eat, he witnesses yet another argument between Asuka and Shinji. Shinji usually makes lunch for both of them, but has failed to do so today, which irritates Asuka to no end, while Shinji tries to defend himself with the fact that he had a lot of homework yesterday. "What's this, a husband and wife quarrel?" says Toji out loud with no shortage of snark in response to the squabble, much to the amusement of the class. Asuka and Shinji falls completely silent in embarrassment for a moment, before both of them frantically deny the notion in perfect unison.
Risuko reveals the news about the Fourth Child to Misato, who is shocked from seeing the identity of the new pilot. Ritsuko then reveals to her that every single member of Asuka, Shinji, and Rei's class is a potential Eva pilot candidate, and they are all kept together for their own protection. Misato remarks that while Asuka and Rei will probably have no problems with this, Shinji might not take it well if he was to find out about it.
Toji, in the meantime, is given the bulletins to deliver to Rei by Hikari. As he mentions not being able to go to a girls place alone, Hikaris face lights up as she offers to take him there, but Toji is already in the middle of asking Shinji to walk with him since he knows where Rei lives, and fails to notice her. As they enter Reis room, Toji cant believe that this is a girls room from how messy it is. Shinji starts cleaning up some trash on the floor after they drop off the bulletins. As Shinji does this, Toji remarks on how much Shinjis changed. At first, he thought Shinji was just a jerk who wouldnt do anything for others, but now that view has changed since Shinjis come out of his shell a little. Rei walks in at this time and Toji explains that theyre just here to drop off some stuff. Shinji points out that he cleaned her room, causing Rei to blush and thank him. She notes to herself that it was the first time she had used those words with anyone. She had not even said it to Gendo.
As Fuyutsuki and Gendo ride on a train to NERV, Fuyutsuki calls Tokyo-3 a paradise built by mankind. Gendo agrees. Man, a weak being and in a world surrounded by death, was forced to use resourcefulness to carve out a niche where he could survive. Fuyutsuki notes that the fortress was finishing its seventh and final construction phase. He then asks Gendo on how he will report the facts to the Committee. Gendo replies that he will simply state things as they are since the cause is truly unknown. As for the loss of the Sengine, Gendo is unconcerned. He says that the data is still in Germany and that Unit 01 and NERVs first branch will suffice for now. He notes with a hint of satisfaction that the unplanned destruction of the second branch should teach the old men at SEELE a lesson, since they are so very obsessed with keeping things going according to their schedule and the Dead Sea Scrolls.
In one of NERV HQ's breakrooms, Kaji has a small drink and a talk with Ibuki. As he begins an attempt to seduce her, Misato walks in causing Ibuki to quickly excuse herself and slide out of the room as fast as she can. Misato chides Kaji for hitting on younger women, causing him to playfully ask if he then could hit on her instead. Misato says that depends on how he honest he can be with her, and starts asking him for some information on Adam and the Marduk Institute. Kaji first tries to evade her questions by playing dumb, but when Misato isn't having any of that, he notices that it is unlike her to ask for help like this. She replies that being her usual self is a luxury she can't currently afford. In response, Kaji pulls her in close, and tells her in a lowered voice that the Marduk Institute doesnt actually exist, but is just a front organisation for NERV, who are really the ones in charge of the whole Eva pilot selection process. He advises her to investigate Code 707 and Misato recognizes that as being the number of Shinjis school before Shinji walks in, interrupting the conversation. As Kaji and Misato both try to act natural, Shinji explains to the latter that Ritsuko wants to see her about a business trip tomorrow. Misato leaves for the meeting, but makes sure on her way out to tell Kaji that they will resume their talk later. After she has left, Kaji asks Shinji if he wants to go out for some tea.
Kaji decides to show Shinji one of his hobbies, and brings him to a corner of the Geofront, where he has a watermelon patch he tends to. Kaji says that he enjoys making something grow, and that it is something that can teach you things and bring you pleasure. Shinji adds that it can bring suffering as well. Kaji asks Shinji if he hates suffering and Shinji replies in the affirmative. He then asks Shinji if he has found something that he brings him joy; but as Shinji seems unable to come up with an answer, Kaji continues, telling Shinji that it is okay if he hasn't found something yet, and explains that he might find that his knowledge of suffering will make it easier for him to be kind to others. As he says that being kind is not a weakness, his cell phone rings and Misato informs him that the sync tests will be starting soon. In the sync test, Shinjis sync ratio is revealed to be dropping. Ritsuko theorizes that it is because of something that happened in Leliels attack while Misato notes that this makes it harder to reveal the identity of the Fourth Child. Ritsuko reminds her that the Fourth Child will be informed officially tomorrow.
The next day, Toji is called to the principals office just before lunch. Kensuke asks him if he have done something to get himself into trouble, but Toji answers puzzled as he prepares to leave for the office that nothing comes to mind. While Shinji and Kensuke finish up lunch on their own, Kensuke reveals some information that he picked up during his trip to New Yokosuka. Namely that Unit-03 is going to be activated in Matsushiro. He also tells Shinji of the destruction of Unit-04 and the second branch, and overtly tries to probe Shinji for more information on these subjects. Shinji notices that Misato didnt tell him any of those things and realizes that he actually feels a bit irritated about not being told, and while Kensuke is shocked to learn that Shinji hasn't heard about these happenings, he still tries to reassure him, saying that she probably didn't tell him because the information doesnt directly affect the pilots. Toji returns during class, clearly troubled. As he eats lunch after school, Hikari comes to him. She tells him of how she cooks every morning for her two sisters and Toji picks up what shes getting at and offers to help with the leftovers.
Late that afternoon, inside NERV HQ, Asuka stands before the door to Kaji's office with a gloomy look on her face. Taking a deep breath, she musters up all her determination, and then opens the door and greets Kaji with her brightest smile and her best cutesy voice. Kaji, however, is busy with his work and offhandedly tries to brush her off, telling her that they can talk later. Asuka surly protests that he always finds time for Misato, and then cheerfully glomps him from behind, much to his annoyance. Asuka then catches a glimpse of the data on his screen, and realizes to her surprise that it shows four synch data reports. Reading further, she discovers the identity of the Fourth Child, and makes no effort to hide her shock and anger. Meanwhile, Eva Unit-03 is readied for take off in America. Elsewhere, Hikari is humming happily to herself as she cooks something up in the family kitchen. Toji is alone on the school basketball court, with a look of woefulness on his face he shoots a goal.
- Call to Agriculture: Kaji tending to his melon patch.
- Like an Old Married Couple: Toji think as much of Shinji and Asuka's arguments.
- * You Called Me "X"; It Must Be Serious: A variation. When Misato directly asks Kaji for his help and doesn't respond to his joking flirting or buy his attempts to play dumb, he releases that Misato is actually serious about needing to talk shop with him, so he quickly drops his usual mellow and jovial attitude and begins to answer her questions in a straight-forward and honest manner.