[1999]
Kouzou Fuyutsuki, an instructor at Kyoto University, meets Yui Ikari, a student there. When Gendo Rokubungi is taken into custody at the local police department for violent behavior, he specifies Fuyutsuki to be the one he is released to. Fuyutsuki's first impression of Gendo is that of distaste.
In autumn, Fuyutsuki is told by Yui that she is romantically involved with Gendo. She says that he is a sweet person.

[2000]
September 13, the Second Impact occurs at the South Pole. The great icy continent melts in no time at all, and the rising water level washes away all sorts of organisms from the land. The twisted axis of the Earth drastically changes the Ecosystem. Furthermore, the civil wars, that ensue, lead to the death of half the total human population. Sights like that of an apocalypse blanket the Earth.
The Katsuragi Research Team visiting the South Pole is wiped out except for Dr. Katsuragi's daughter, Misato. Gendo, who had been part of the same research team, had left the day before the unfortunate event and escapes the calamity.

[2001]
Yui and Gendo's first child, Shinji, is born. Gendo had intended to name the child "Rei" if it had turned out to be a girl.

[2002]
Fuyutsuki had been working as an unlicensed doctor, but at the U.N.'s request, he heads for the South Pole to conduct a formal investigation into the Second Impact. Fuyutsuki meets Gendo there again and learns that he and Yui are now married and have a child. Fuyutsuki confirms his suspicions that SEELE, the organization that Gendo belongs to, is covering up some vital facts regarding how the Second Impact occurred.

[2003]
Fuyutsuki continues to investigate on his own, and it leads him to Gendo Ikari, the director of the Artificial Evolution Laboratory (AEL). Fuyutsuki visits the laboratory and threatens to go public with the truth, but Gendo leads him to a giant space - Central Dogma - sprawling beneath the laboratory. There, he finds Dr. Naoko Akagi, a leading authority on bio-computers, and learns that they call themselves GEHIRN. Furthermore, the half-built Evangelion Unit-00 could be seen there as well. Gendo says to Fuyutsuki, "Work with me to create a new era in the history of mankind." After carefully thinking it over, Fuyutsuki accepts the invitation.

[2004]
During an experiment in Underground Laboratory #2 in Hakone, Yui Ikari vanishes. It is an accident that occurs right before her son, Shinji. Immediately afterwards, Gendo goes missing, and Fuyutsuki becomes gravely concerned at the week-long absence of the commander. What happened during this time is obscured and unclear, but when Gendo returns, he informs Fuyutsuki that he is endorsing the "Human Instrumentality Project" and the "Adam Regeneration Project." Later, Naoko Akagi says that Gendo changed after this time period.
At around the same time, Gendo places Shinji in the care of an acquaintance. After that, Shinji would live apart from his father until the year of 2015.

[2005]
Five years has found Misato recovered (though not completely) from her aphasia. At Tokyo-2 University in New Tokyo-2, she makes the acquaintance of two people. One is Ritsuko Akagi, daughter of the distinguished Dr. Naoko Akagi. The other is Ryoji Kaji, a man who has something of her father in him. Kaji and Misato eventually move in together.
Asuka Langley Sohryu is chosen as the Second Child. On the same day, her mother, Kyoko Zepplin Sohryu, who had previously already been in a mentally broken state, hangs herself in the hospital.

[2007]
Misato and Kaji break up. The reason is within her heart. Kaji was too much like Misato's father.

[2008]
The fundamental theory for the bio-computer Magi is completed by Dr. Naoko Akagi. The procurement of the Magi represents further progress in Gendo's plans.
Ritsuko Akagi joins Gehirn after graduating from her university. She is assigned to Project E, placing her in the same department as her mother. However, due to this, she finds that her mother and Gendo are involved with one another.

[2009]
Misato Katsuragi joins Gehirn. Her post is Germany's Branch 3.

[2010]
Rei Ayanami (the first) arrives at Gehirn. Gendo, who accompanies her, explains that she is a friends daughter.
Dr. Naoko Akagi's efforts bring the Magi to completion. The same night, Naoko learns from young Rei that she is nothing more than a tool to Gendo to realize his plans. In a passionate outburst, she strangles Rei to death, then throws herself from the command center to her death as well. The next day, SEELE decides to dissolve Gehirn, which had been the Human Instrumentality Project's research organization. All members of the organization are transferred to the special duty organization NERV, which would carry out all projects. SEELS's plans enter a new phase.

[2012]
The 8th anniversary of Yui Ikari's death. Shinji visits the grave with his father, Gendo, but he runs away from the bodiless grave and disappears.

[2014]
Rei Ayanami (the second) transfers to New Tokyo-3 Public Middle School 1.

[2015]
Summoned by his father, Gendo, Shinji Ikari comes to New Tokyo-3. On the same day, an Angel attacks for the first time in 15 years. To mankind, it is the third they have encountered - the Third Angel. For the sake of New Tokyo-3's defense, Shinji is hastily put on board the artificial human Evangelion. He narrowly manages to intercept the Angel and demonstrates his talents in his first battle.
From then on, there is a rash of Angel attacks. NERV also responds by sending first Unit-00 (First Child - Rei Ayanami), then Unit-02 (Second Child - Asuka Langley Sohryu) to battle.
At the same time as Unit-02's addition, Ryoji Kaji of NERV's Special Inspections Department comes to Japan. He brings "Adam" with him to NERV Headquarters.
Branch 2 of NERV in America vanishes. It is surmised that it is due to an accident that occurred driung the experimental installation of a S2 engine onto Eva Unit-04. Horrified by this incident, America decides to fly Eva Unit-03 over to Japan from America's Branch 1. As for the pilot of that unit, the Fourth Child = Toji Suzuhara is newly selected. However, Unit-03 is infiltrated by an Angel during the transport and goes out of control during the activation test. It is dispatched as an Angel by Eva Unit-01. After this operation, the Unit-01 pilot, Shinji Ikari, voices his objections regarding how the operation was conducted and rebels against his father.
Through private appropriation of Unit-01, he tries to threaten his father but ends in failure. The Third Child's entry is erased for a time, but he returns to the front line when the Fourteenth Angel invades NERV Headquarters. He successfully intercepts the Angel. Furthermore, Unit-01 goes berserk during the battle, preys upon the Fourteenth Angel, and acquires the S2 engine.
Kaji, who had been making private inquiries into NERV under order from SEELE, is shot and dies.
In the fight against the Fifteenth Angel, Gendo orders the use of the Spear of Longinus. Unit-00's attack with the Spear successfully brings down the Angel, but the Spear goes as far as the moon and becomes unrecoverable.
Eva Unit-00 blows itself up in order to defeat the Sixteenth Angel. The pilot of said unit, Rei Ayanami (the second), perishes. Rei Ayanami (the third) goes into action.
The person in charge of Project E, Dr. Ritsuko Akagi, defects. She destroys all of the dummy plug Rei Ayanami individuals, except for those that were in operation. The true reason behind this is her complicated love-hate relationship with Gendo Ikari.
Asuka runs away. She is secured without incident, but she was no longer in any condition to pilot the Eva.
As a replacement pilot for Asuka for Unit-02, the Fifth Child = Kaworu Nagisa arrives via the Human Instrumentality Committee. However, his true identity is a humanoid Angel. This Angel successfully enters Terminal Dogma, but the Third Impact that people had feared would happen did not occur. He is throttled to death by Unit-01 which came after him.


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