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, 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. Meeting her in his office he asks 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 man with a reputation for being a violent hothead, 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 years 2000 and 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 the 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 to see the work being done at the laboratory. A puzzled Fuyutsuki reluctantly agrees. 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." They reach their distination, 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, and her work on the new MAGI computer system. He is also shown a prototype Evangelion which he first mistakes for Adam. Gendo now invites Fuyutsuki to join his new organization, GEHIRN, and help it create a new future for 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 normally carries. She has learned from Misato that she 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 supports "her ideal's, not SEELE's", and is willing to help her. He mentions that he cannot do anything rash since SEELE views him as expendable and keeps him on a short leash. He also warns her about the contents of the Dead Sea Scroll and how they can lead to a Third Impact within the next decade. He advises her against following her plan 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 in a tight embrace, revealing them to be having an affair. They do not notice her.
It is now 2010, and Gendo arrives at work with the company of a little girl. Naoko asks about her, wondering what happened to Gendo's son. Gendo tells her that the child’s 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. Ritsuko tells her that she will be leaving early to pick up Misato, who has recently broken up with Kaji and is now another member of GEHIRN. Naoko pulls a late shift, as Rei suddenly appears in control room. Naoko is puzzled by this, and ask if they should go look for Gendo. Rei responds by calling her an "old hag." Miffed, Naoko tells her that she can't talk that way to other people, but Rei responds that it is what Gendo calls Naoko: a useless old hag. Realizing that Gendo never truly loved her, Naoko snaps and strangles Rei in her anger. Coming back to her senses and seeing what she has done, Naoko panics and commits suicide by jumping out from the MAGI control tower. Ritsuko did not find out until the next day. That same day, GEHIRN was disbanded and 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 is already the problem since they have figured out that he delivered the Adam sample to Gendo. His only goal now is to find the truth. 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.
Having arrived back at the apartment, Misato 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." 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.
- A Day in the Limelight: The episode is mainly this for Fuyutsuki, but other characters get quite a bit of attention too.
- Dead Man Writing: Kaji's phone call to Misato.
- 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.