Synopsis

Vice-Commander Fuyutsuki has gone missing, and Misato is held captive with Kaji as the prime suspect. Fuyutsuki is being questioned by SEELE, who recounts his first involvement with Yui Ikari and Gendo Rokubungi and the events afterward. The histories of Misato, Ritsuko and Professor Akagi are also recounted.

Full Recap

Kaji tries to ring Misato, but she's not there. Misato is called by authorities and is asked to take care of business.

Fuyutski is called by SEELE, and the professor remembers the last time he was called professor. He met a student named Yui Ikari about a paper.

2015 AD: SEELE begins thinking of creating an Evangelion.

1999 AD: Fuyutski first meets Gendo Rokubungi and he doesn't like him. But Yui has other thoughts and thinks of marrying him.

The second impact occured in 2000 AD and in Antartica, Gendo shows Fuyutski a postcard revealing that Gendo changed his name to Ikari, and that they have a child.

2015 AD: Misato is sitting alone.

Young Misato is mute and sitting in an empty room recovering from the Second Impact.

2003 AD: Gendo is questioned about the Second Impact. But Gendo just shows to Dr. Fuyutski the Geofront, and he meets Dr. Akagi and her daughter, Ritsuko. Dr. Akagi shows Fuyutski an Evangelion protoype and Gendo asks if he will join them in Project E.

Misato and Ritsuko were friends in college and is shocked by her past. Ritsuko is writing a letter to her mother and she is replying.

Young Shinji is watching the start-up process of the Evangelion and Yui dies in the process. Gendo is tragically upset and changes.

Ritsuko joins and begins on Project E. Dr. Akagi kisses Gendo when he is grieving over Yui. Gendo turns up with a young girl and claims that she is the daughter of an acquaintance named Rei Ayanami, but Dr. Akagi is suspicious.

Dr. Akagi finishes the Magi system. She is then visited by Rei who calls her an 'old hag' and annoys her. Dr. Akagi goes mental and she chokes Rei to death. She then commits suicide in front of the Magi System. NERV was formed.

Fuyutski is visited by Kaji who sets him free.
Misato is offered a gun and she has no choice but to follow the authorities orders. Kaji is waiting and then is shot.

Misato returns home and sees a message from Kaji on the answering machine. She listens to it and begins crying. Shinji, not knowing what to do, just sits there, listening to his music and trying to not listen to her crying.