Two classified security recordings from the Katsuragi Expedition on Antarctica are shown. In the first from August 15, 2000, the scientists marvel at their discovery of Adam, while Chairman Keel and Gendo are having a conversation. Keel considers the scientists to be too selfish of nature to accurately assess reality; they are too concerned with self-gratification, and do not fully appreciate the joy of discovery or the power of knowledge. The second takes place on the day of Second Impact: Adam awakes, and despite the desperate attempts to contain him, he rises as a giant of light.
Back in the present, Kaji calls Misato from a phone booth, but gets her answering machine. After leaving a message, he tells himself that his next undertaking will be probably his last mission. Later, Misato is told by two of NERV's security agents that Fuyutsuki has been abducted, and that Kaji is the main suspect. Because of her relationship with him, she is also under suspicion, and she willingly goes into custody until the case is solved.
Meanwhile, Fuyutsuki sits in a dark room handcuffed to a chair. He is greeted by Chairman Keel, who speaks to him through a holographic presence in the form of an anonymous black monolith marked with the number 01. As several other holographic monoliths appear in a circle around him, Fuyutsuki realizes that he is speaking directly to SEELE's leadership and not the usual Human Instrumentality Committee. SEELE explains that they want to interrogate him on the trustworthiness of Gendo following the latest worrying developments with Unit-01. Upon being referred to as "professor" once again, Fuyutsuki starts to reminisce about the past.
In the year 1999, Fuyutsuki is a teacher in Metaphysical Biology at Kyoto University. Through a colleague he hears about a promising new student in bioengineering named Yui Ikari, who is interested in his work and wants to meet with him. As he meets her in his office, their conversation about science eventually leads Fuyutsuki to ask Yui what her long term plans are, and she admits that she actually wishes for a quiet domestic life if she meets the right guy, both surprising and intriguing the professor. Through Yui he also meets the student Gendo Rokubungi, a young man with a reputation as a hotheaded troublemaker who often gets into fights, and Fuyutsuki does indeed dislike him from their first meeting. But Gendo himself has no problems with Fuyutsuki's outspoken dislike; he comments that he is used to being hated.
Fuyutsuki becomes close friends with Yui and when she tells him that she is dating Gendo, he finds it hard to hide his displeasure and concern. However, she reassures him that Gendo does have a nicer side; it is just hidden so almost no one sees it. Fuyutsuki relates about his suspicions of Gendo's ulterior motives: that he is only going after Yui because of her connection to the mysterious and powerful organization SEELE, which backs her research. He does not voice them to her, however.
Second Impact strikes, casting the world and humanity into chaos and war, which turns the rest of 2000 and the entirety of 2001 into what Fuyutsuki can only describe as a "pure hell." In 2002, during the aftermath of the Second Impact, Fuyutsuki has taken up work as an unlicensed medic in a makeshift clinic in the flooded ruins of Toyohashi City. He is contacted by a government agent on behalf of Gendo, who wants him to join an UN headed investigation of Antarctica.
On the ship headed for Antarctica, Fuyutsuki meets with Gendo and expresses his surprise at the latter's survival, noting the extreme luck of his team leaving Antarctica just before Second Impact. He is then appalled to learn that Gendo now has Ikari as his surname, as he has married Yui and has a son with her. Getting back to business, Fuyutsuki expresses concern about the mission being supported by SEELE, as he has heard bad things about the organization, but Gendo brushes him off, telling him that no one can accomplish anything by being honest these days.
Back in the present, Misato huddles in the confinement cell as the dark bring back bad memories. In 2002, Fuyutsuki observes a younger and clearly catatonic Misato in a cell. He is told that she has not spoken in two years. Fuyutsuki also learns quite a few scary things about the post-impact Antarctica, namely that all natural life in the area, down to the micro-organisms have been obliterated, that there apparently is a dome shaped cave under the blast side, and he hears the disturbingly substantial rumors of a humanoid giant of light rising over the camp shortly before the explosion. Despite these facts, Second Impact is covered up as freak meteor strike upon the expedition's return, but Fuyutsuki quickly realizes that SEELE is behind this.
In 2003, Fuyutsuki goes to The UN Artificial Evolution Laboratory in Hakone, Yui and Gendo's new workplace, and confronts the latter with evidence incriminating him and SEELE as being responsible for Second Impact and its cover-up. He also tells him that he knows about the secret Dead Sea Scrolls and threatens to go public with everything. Gendo is unmoved, even somewhat amused by Fuyutsuki's threats. Apparently taking it all in stride, he casually invites him down to the laboratory so he can see the work being done there for himself. Though distrustful of Gendo and puzzled by this act of joviality, Fuyutsuki's curiosity wins out and he accepts the invitation. The two of them boards a tram which takes them deep down into Hakone's underground, and Fuyutsuki notices on the halfway that they are heading into a dome shaped cave not unlike the one on Antarctica. Gendo tells him that they indeed are similar and that they were "left behind, by someone who was not us." Upon this revelation, a shocked Fuyutsuki asks Gendo if SEELE is intending to repeat what happened on Antarctica, but Gendo merely answers that it is up to himself to decide if that is the case.
They reach their destination, a laboratory complex build on the floor of the dome, and here Gendo introduces Fuyutsuki to Naoko Akagi, a genius in the field of computers, who is busy working on a project. Fuyutsuki, already somewhat familiar with Naoko and her work, asks her what has brought her to this place. She tells him that the lab is the best place to test out fundamental theories for the bio-computers of the future, and she is currently working on creating a new kind of supercomputer, which she wants to name the "MAGI". Fuyutsuki asks Gendo if this is what he wanted to show him, but Naoko tells him that Gendo had something else in mind and proceeds to guide them on to another part of the facility (telling a young and very awkward Ritsuko in passing that she will be back later). In a huge dark hall, Fuyutsuki gets quite a shock when the lights come on and he is face to face with a prototype Evangelion, which he first mistakes for Adam. Gendo tells him that the giant is a part of the Adam Revival Project, generally known as "Project E", and what he is currently looking at is the prototype for the project, Unit-00. "A prototype for a god?!" asks Fuyutsuki, at which point Gendo reveals to him why he has taken him here as he invites him join his new organization, GEHIRN, and work with him to usher in new era in the history of mankind.
In 2005, Misato and Ritsuko meet for the first time at college in Tokyo-2. Ritsuko relates the experience to Naoko in a letter, noticing that Misato has quickly become her best friend, since she so far has been the only fellow student who treats her without the reservations her prestigious family name normally carries. She has also learned that Misato is the sole survivor of the Katsuragi Expedition and apparently was a mute for some years, though Ritsuko finds the latter a bit hard to believe, since Misato always chatters away a mile a minute as if to make up for lost time. Later, she writes about Misato's new boyfriend, Kaji, and how him and Misato had skipped an entire week of classes to stay in bed together.
Fuyutsuki and Yui meet near a lakeside in Hakone in 2003. Yui brings along a young Shinji. Fuyutsuki tells her that he has personally seen the Secret Dead Sea Scrolls, and they said that Third Impact will definitely happen in a little over ten years, and he declares that he supports "your intentions, not SEELE's", and is fully willing to help her. He mentions that there is the caveat that he is going to have to rely on Gendo's cooperation, as he neither do it alone nor do anything too rash since SEELE views him as expendable and keeps him on a short leash. Yui sadly comments that it is easy to have people eliminated these days. He answers that is still a bad reason for her to become a test subject in the EVA project, but Yui tells him that she must follow through and go with SEELE for Shinji's sake.
In 2004, GEHIRN is prepairing to conduct a contract experiment on Unit-01 with Yui as the test pilot. The young Shinji is present, much to Fuyutsuki and Naoko's annoyance, but Yui says that it was her idea. She wanted to show her son "how bright the future seems." This turns out to be her last words, as the experiment goes haywire and she is absorbed by Unit-01 without a trace. Attempts to retrieve her are met with failure. Naoko notices that the event changes Gendo completely. He isolates himself for a week and refuses to talk to anyone during that time. As Gendo comes back to work Fuyutsuki tells him that he is right to grieve, but there are also tasks to be done. Gendo answers that he has already thought about this and that he has just purposed a new plan to Chairman Keel, the Human Instrumentality Project.
In 2008, Ritsuko arrives at GEHIRN's headquarters to start working on the MAGI. She gets lost in the complex and accidentally walks in on Naoko and Gendo engaged in a conversation. Undetected by the two, Ritsuko listens in from the shadows and overhears hears Naoko accusing Gendo of being unable to let go of Yui, before she ends their conversation by saying that she doesn't mind this and then starts kissing him, revealing the two to be in an affair.
It is now 2010, and Gendo arrives at work with the company of a little blue-haired girl. Naoko asks about her, wondering what happened to Gendo's son. Gendo tells her that the childs name is Rei Ayanami and he is looking after her for a friend. Naoko privately notices that the girl is a dead ringer for Yui. She later checks Rei's file but finds literally nothing on her.
Later that year, Naoko and Ritsuko have completed the work on the MAGI. Naoko explains to Ritsuko how she has incorporated three aspects of herself into the computer, and how pretty much all there is left to now is to turn on its power. Ritsuko tells her that she will be leaving early to pick up Misato, who has also started working for GEHIRN, as she is coming back to Japan tonight after having worked some months at GEHIRN's 3rd Branch in Germany. Naoko comments that it must mean her relationship with Kaji has been on long distance for a while, but Ritsuko answers that last she heard, they broke up. This surprises Naoko, who thinks that Misato and Kaji seemed like such a nice couple, to which Ritsuko comments that you can never tell with relationships between men and women as they refuse to conform to any kind of logic. Half-joking, half-serious, Naoko warns Ritsuko to be watchful about her cold attitude, lest it allows her happiness to slip away from her. "Happiness is even harder to define," answers Ritsuko with a hint of melancholy, before mother and daughter bid each other goodnight. Now alone in the control room, Naoko turn to finish up some work, but is startled when Rei is suddenly present in the room. Naoko is puzzled by this, and ask if they should go look for Gendo. Rei coldly answers she can find home by herself and calls Naoko an "old hag." Miffed, Naoko tells her that she can't talk that way to other people and she will tell this to Gendo, but Rei responds that it is what Gendo himself says about Naoko when she is not around; he calls her a pushy and useless old hag and says he doesn't need her any more. Realizing that Gendo never truly loved her, Naoko snaps and strangles Rei in her anger, telling her "It doesn't matter if you die, you can always be replaced, Rei... The same as me." Coming back to her senses and seeing what she has done, Naoko succumbs to despair and commits suicide by jumping out from the MAGI control tower. Ritsuko did not find out until the next day. That same day, Chairman Keel put out an order to disband GEHIRN and had it restructured into NERV.
In the present, Kaji breaks into the room where Fuyutsuki is held by SEELE and frees him. Fuyutsuki warns him that SEELE will want him dead now, to which Kaji says that he is already aware of that, as he knows that by now they must have figured out that he was one the delivered the Adam sample to Gendo. All he wants now is to get closer to the truth within himself and protect his own interests. Later, Misato is released as Fuyutsuki has been found again. She asks the NERV agent about the whereabouts of Kaji, but he denies any knowledge.
Standing against a wall in an industrial building lit by the setting sun, Kaji notices someone. He calmly greets the unseen person with, "Hey, you are late, soon before a shot echoes through the building.
Night has fallen and Misato arrives back home at the apartment. She notices that there is a message on the answering machine. It turns out to be from Kaji. He apologizes for the trouble he has put her through, and urges her to continue to seek the truth about NERV, before ending his message with "If I ever get to see you again, I'll say the words I wasn't able to say eight years ago. Bye." As she comes to the realization that Kaji is dead, Misato breaks down in sorrow. Shinji hears her in his room and considers for a moment to go into the kitchen and comfort her, but finds himself too scared do it. He opts to stay in his room instead, telling himself that he is, after all, just a child.
- The Call Left a Message: Implied Trope. Gendo's nonchalance and utter lack of surprise when Fuyutsuki confronts him with the evidence of his and SEELE's involvement in Second Impact, seems to at least indicate that Gendo deliberately left it out in the open for Fuyutsuki to find, so that he would follow the trace to GEHIRN, thereby giving Gendo the chance to recruit him into the organisation.
- Closest Thing We Got: During his stint as a unlicensed medic, Fuyutsuki admits that his skills as a medical doctor are limited and the conditions he runs his makeshift clinic under are pitiful, but with the dire need for medical personal everywhere he feels he has to help where he can.
- A Day in the Limelight: The episode is mainly this for Fuyutsuki, but other characters get quite a bit of attention too.
- Cold Open: The Director's Cut version opens with video footage recapping the second impact, followed by the series' opening proper.
- Dead Man Writing: Kaji's phone call to Misato.
- Double Meaning: On closer inspection, Fuyutsuki and Yui's brief conversation during the contact experiment is laden with this. Fuyutsuki is the only one in the room who already knows that Yui is planning to get absorbed by Unit-01. He, however, is caught off-guard by the facts that Shinji is present as spectator for the experiment and that Yui was the one had the idea to bring him there:Fuyutsuki: (to Gendo) Ikari, this is not a nursery school. Today is a crucial day!
Yui: I'm sorry, Professor Fuyutsuki. I'm the one who brought him.
Fuyutsuki: (with more than a hint of misgiving in his voice) ...Yui, this is your experiment today. (We both know what you're just about to do. Do you really want your son to see this?)
Yui: That's why. I want to show my child the bright future. (Yes, I'm sure he needs to see this.)
- Dull Eyes of Unhappiness: The catatonic Misato in the 2002 flashback has these.
- Dumb Struck: The young Misato didn't speak for a couple of years while she recovered from her experiences during Second Impact. A pretty understandable reaction to witnessing both the death of her father and what was almost the end of the world up close.
- Dying Declaration of Love: Those "words I wasn't able to say eight years ago" Kaji mentions are strongly implied to be something along the lines of "I love you. Will you marry me?"
- The Reveal:
- Everything about Yui's introduction scene. The viewers are first teased with Fuyutsuki hearing about a promising young student named "Ikari", who wants to meet him, and are mostly likely expecting it to be Gendo. The scene where Fuyutsuki actually meets the student, however, goes on to reveal that said Ikari is actually Yui, who has mostly been kept as a mysterious, unseen figure up until this point, and then pulls another twist on top of this, by giving us the first real good look at her, revealing that she has an eerily close resemblance to Rei.
- After this follows the real introduction of Gendo, giving the viewers the minor, but still quite important reveal that he used to be the somewhat unremarkable student Gendo Rokubungi, and got the name Ikari through his marriage with Yui.
- Present Tense Narrative: The ending briefly engages in this, with Shinji reflecting on how he felt helpless when confronted with Misato's grief and didn't knew how to help her. It implies that this is Shinji, much later in his life, reflecting back on the events that happened then.
- Riddle for the Ages: The identity of Kaji's killer.
- Secret Society Group Picture: A somewhat unintentional version. Fuyutsuki studies the official press photos from the hearing on Second Impact, and notices Gendo and Keel Lorenz (and, it is implied, other prominent members of SEELE) lurking in the background of several of them.
- Shout-Out: In the classic ADV English dub, as they're descending into the underground, Gendo says to Fuyutski, "Are you worried, Montresor?" Strangely, in the Poe story, Montresor is the murderer who lures his erstwhile friend into the wine cellar.
- Sound-Only Death: Kaji's death is indicated by a Smash to Black followed by the sound of a gunshot.
- Take Our Word for It: The year of 2001 was apparently so utterly horrible to live through that Fuyutsuki doesn't want to remember it in any great detail."The first year of the 21st century was pure hell. There is no other word to describe that year."
- The Teaser: The Director's Cut version of the episode starts with the showing of the classified security tapes, before cutting to the opening title.
- Troubled Fetal Position: Misato assumes this position inside NERV's confinement cell, as she is struggling with bad memories of being in such a place. The episode then cuts back to the past, showing her younger self, sitting in the exact same position, in a similar cell.
- Wham Shot:
- The first appearance of the iconic SEELE monoliths during their 'chat' with Fuyutsuki. We're now seeing the true power behind NERV and even the Committee.
- The reveal of Yui Ikari, especially the fact that she uncannily resembles Rei.
- Whole Episode Flashback: The episode spends most of the time laying out the backstories of most of the adult cast, as well as the backstory of NERV itself.