In the aftermath of the incident involving Zeruel, the Human Instrumentality Committee is shocked to find out that Unit-01 was able to eat and absorb an Sengine from an Angel, something they thought was impossible, and they notice they never actually planned for anything like that to happen. They discuss Gendo Ikari and how it might have been a mistake to make him the leader of NERV. Chairman Keel, while also quite concerned about the developments, reminds them that without Gendo, they could not have achieved their goals.
Meanwhile, NERV tries to pick up the pieces from the devastating attack. Units 00 and 02 are both severely damaged and undergoing emergency repairs, while Ritsuko, Ibuki, and Aoba discuss the move to a new command center. The MAGI system can be backed up there and operations can resume as usual. "At least we have an alternative," Ritsuko states darkly. "We have no choice when it comes to using Unit-01."
Unit-01, after its rampage, lies restrained in its cage, its face wrapped up in bandages so that only a green eye remains glaring. Misato is reassured by Hyuga that there is no activity present within the unit so it is securely held by its restraints. Misato reminds him that nevertheless, Unit-01 has on three occasions been able to move without any active power sources, so they can't allow themselves to be careless.
The Instrumentally Committee evaluates the damage to NERV HQ and the EVAs from the attack, concluding it will cost them huge amounts of time and money. They question the reliably of their spy inside NERV, pointing out that he failed to warn them about the developments they are now facing, agreeing they must make absolutely sure that they will be warned next time. Meanwhile, Kaji asks Gendo how hes going to face the Committee with all that has just happened. Gendo responds that he will claim that the whole thing was an unexpected accident, seeing how Unit-01 was not under NERVs control and that the Eva will remain frozen until further notice. Kaji points out that, while it probably is an appropriate decision, Shinji is still trapped inside the EVA.
All attempts to recover the pilot of Unit-01 have failed. In fact, when the video feed into Unit-01 is reestablished, Shinji is no longer inside the cockpit which Ritsuko attributes to the fact that he is inside the Eva. As Misato angrily asks what exactly an Eva is, Ritsuko simply says that it is something man created in mans own image. Misato then asks if the Eva is only a copy of what they once found on the South Pole, but Ritsuko answers that the Eva is not just a copy, but a creature "imbued with a human will." "Are you saying somebody willed this to happen?!" says Misato appalled. "No, the Eva did," answers Ritsuko vaguely. As Ritsuko doesnt show any signs of helping get Shinji out, Misato loses control and slaps her, demanding that she take responsibility for the thing she helped create.
Rei in the meantime awakens in the hospital, surprised that she is still alive. Asuka could not care less upon hearing the news. She lies in bed, frustrated and on the verge of tears at having to be saved by Shinji again. Her room is in shambles as broken cups, ripped up magazines, and personal belongings are strewn across the floor.
On the third day after Zeruels attack, Ritsuko comes up with a plan to rescue Shinji. Misato is skeptical and clearly still angry at her, but listens to the plan. Shinji is still inside the entry plug, however his body has lost its form. This is a consequence of achieving a high sync ratio with the Eva. He has basically disintegrated and his consciousness is now floating around in the LCL. What has to be done now is return his body to physical form and put his soul back into it.
Meanwhile, inside Unit-01, the disembodied Shinji floats around in a dreamlike state, and thinks to himself about why he fights and who the real enemy is. As visions of Angels flash before him, they start turning into images of his father. Shinji balks at the sight of Gendo, accusing him of hurting Toji and killing Yui, as he draws Unit-01's progressive knife and angrily lunges at the image. He is interrupted by a vision of Rei, who asks him if he really understands his father. Shinji responds that of course he can't understand Gendo since he hardly sees him. She then asks Shinji if that is the reason he hates his father. Which Shinji affirms, his father doesn't need him and deserted him. Rei asks if that makes her the substitute. "That's got to be it," exclaims Shinji, "He abandoned me because he had you!" "As if you didn't run away all by yourself," answers Rei. Shinji then relives the moment he first saw Unit-01 and when he asked his father why he was brought here. His father responds saying that he is the only one who can pilot the Eva.
But then the memory starts to alter. Shinji states that his real reason for coming to Tokyo-3 was to tell Gendo that he hated him, and he now hears himself asking his father if the real reason for making him pilot the Eva is to make him suffer, which Gendo confirms. Shinji then hear himself repeat that he has never seen the Eva before. But he has come to realize that what he said back then wasn't entirely true. In his new state of mind, Shinji now knows that he had seen Unit-01 before. He can remember fractured glimpses from years ago, being a young child observing something happening. "I knew the Eva," he says. He remembers that back then he ran away, "Leaving my father and mother behind!"
The thirtieth day after Zeruels attack arrives and Unit-01s armor has been restored. Ibuki marvels at the plan that Ritsuko was able to piece together, until Ritsuko reveals that most of the plan was salvaged from a similar one ten years ago. The incident happened during Naoko Akagis term at NERV. When Ibuki asks how it went, Ritsuko reveals that the operation failed.
On the thirty-first day, Shinji continues his introspection inside the entry plug. He converses with an apparition of Rei, and she asks him why he pilots the Eva. He answers that it is the only way he can justify his existence. It is his reason for living. Everyone acknowledges and praises him when he pilots the Eva, so he has to do it. He has to fight those who are called the enemy and he has to win. Otherwise, he would be alone again and his life would be meaningless. As he imagines everyone egging him on to work harder, he tries to plead with the voices, telling them that he is working hard. As no one seems to listen, he screams and asks why no one can just be nice to him. "I am nice to you," answers Misato's voice.
Visions of Misato, Asuka, and Rei then flash through Shinjis mind. Each vision asks if he would like to become one with them. As the visions combine together, they encourage him to release his soul. Meanwhile, on the outside, the salvage operation commences; probes are inserted into the entry plug and the personnel starts transmitting signals to the EVA. Shinji notices the signals, but is seemingly unable to fully comprehend them, interpreting them as greetings from his friends. It soon becomes clear to Ritsuko that the signals are not working as intending. Misato asks what that means; "It means we failed," replies Ritsuko darkly as she orders the team to immediately reverse the process. But it is apparently too late, as strange readings come from the plug. "What is this?" Ritsuko asks quietly. "Don't you want to come back, Shinji?" Shinji, meanwhile, mumbles confused that he doesn't understand what is happening. Visions of Misato, Asuka, and Rei appears to ask him what he wishes for, before a vision of his mother finally appears with the same question. On the outside, all signals going into the Eva are blocked and soon, the entry plug opens up on its own. The LCL inside spills out along with Shinjis empty plugsuit. Misato runs out and picks up the plugsuit, cradles it her arms and asks on the verge of tears what good science is if it can't even save one life, before she turns towards Unit-01 and angrily shouts "GIVE ME BACK MY SHINJI!" at it.
Back in the entry plug, Shinji asks himself what he wants and where he is. A vision of his childhood self tells him that he is inside the Eva. He asks why and how he ended up there. He remembers not wanting to pilot the Eva. A vision of Misato then tells him that whether or not he wanted to, Shinji did indeed pilot the Eva. Now Shinji has to choose whether he will go through that again or whether he will stay in this inner world, forever in limbo.
Shinji then remembers a smell. A human smell. He remembers then that it is the smell of his mother. He remembers a conversation between Gendo and Yui where Gendo asks her whether Shinji should live in this hell that the Earth has turned into. Yui says that while he is still alive, he can have a chance to achieve happiness. Shinji finally hears a conversation from before his birth, where Yui asks Gendo if he has decided on a name for their yet-to-be-born child. "If it's a boy, Shinji. If it's a girl, I'll name her Rei," sounds Gendo's answer. Guided by his mothers voice, Shinji materializes, alive but unconscious, from the pool of LCL, in front of a sobbing Misato.
Two days later, Misato drives Ritsuko home. On the way there, Misato expresses that she is thankful to have Shinji back, but Ritsuko admits to her that she believes her method actually failed, and it was Misato who truly helped bringing Shinji back from the brink. She also shares some rumors she heard about the Committee freezing the Evangelions forever. Ritsuko then asks Misato if she wants to go out for a drink, but Misato says she can't, vaguely stating that she has somewhere to be tonight, before dropping Ritsuko off and bidding her goodbye. But Ritsuko has a pretty good idea what that "somewhere" is. "Going on a tryst with a man the moment she knows that Shinji is safe? I guess I'm in no position to talk," she says knowingly as she watches her old friend driving off.
Indeed, later that evening Misato meets up with Kaji to, in Kaji's words, indulging her carnal desires. As they lie naked together in the afterglow, Misato muses that Ritsuko must not think very highly of her by now. Kaji says that what engaging in one's desires are really just the kind of behavior realistically expected from the average human, and they might be able to fool the others for a while. "You don't have any interest in others, but you want their attention anyway. You really are just like my father," comments Misato. Looking to the ashtray with the remains of Misato's recently smoked cigarette, Kaji says he had no idea she still smoked. Misato answers that she only ever smokes after sex, so he is the only one who has seen her doing it. "Well, I'm honored," says Kaji. Misato then tries probing him for information about Adam and the Instrumentality project, as well as Gendo and NERV's true objectives. Kaji dodges the questions for a while by pleasuring her, yet he hands her a small capsule in the end. When Misato asks what it is, he replies that it is a present, the first he has given her in eight years, before he grimly adds that it might also be his last one for her.
- Foreshadowing: Quite a bit. Most notably, when Rei asks if she is a substitute, an image of Yui's gravestone is imposed over the line. Hints of exactly what Instrumentality involves are also dropped with things like Shinji becoming LCL, and images of Misato, Asuka, and Rei calling out to him, asking him to become one with them.
- Sex for Solace: The episode ends with Misato meeting with Kaji for sex. Their pillow-talk makes it clear that for both of them it is more or less an attempt to cope with the emotional stress they have been dealing with lately (though they do both also have an ulterior motive for seeking each other out, like Misato trying to pump Kaji for information, and Kaji handing her "a present").