Shinji Ikari is summoned to Tokyo-3 by his estranged father Gendo, commander of the special agency NERV, to defend the city from a giant Angel by piloting the only weapon capable of battling the monster: Evangelion Unit-01.

Shinji wakes up in the hospital, with no memory of defeating the Angel the night before. Rejected by his father, Misato decides to take Shinji with her to live in her apartment. Later that night, memories of the battle against the Angel come flooding back to Shinji.

EVA-00 is finally repaired, and Shinji tries to get to know its enigmatic pilot, Rei Ayanami, better. However, he is confounded because she is extremely insular, has no friends at all, and the entire record of her past has been erased. In the midst of this, a very powerful Angel, the floating monolith Ramiel, attacks Tokyo-3.

Misato brings Shinji, along with Touji and Kensuke, to a massive UN naval convoy transporting Evangelion Unit-02 and its fiery German pilot, Asuka Langley Souryuu, to Japan. Escorting Asuka is Misato's old boyfriend, Ryouji Kaji. After some awkward introductions and reunions, the fleet is attacked by a massive aquatic Angel. Asuka powers up Eva-02, and decides that she will defeat the Angel by playing "hopscotch"...

Asuka joins Shinji’s class at school, and moves in with Misato and him in their apartment. As Asuka adjusts to Japan (or rather, everyone else adapts to her...), a new Angel attacks which is capable of splitting itself into two identical copies. EVA-01 and EVA-02 are defeated, and NERV is publicly humiliated. With the Angel in a week-long regeneration period after an N² Mine attack by the JSSDF, Asuka and Shinji must learn to "synchronize" with each others movements combat, in order to defeat it once and for all.

It seems like it's an important day for nearly everyone at NERV. Misato and Ritsuko are going to a wedding; Shinji and Gendo are visiting Yui's grave; Asuka has a date. However, important things will spring from these seemingly mundane events.

Shinji achieved an unprecedented 400% synchronization ratio with EVA-01 during the battle with Zeruel, to horrible effect. With the EVA having ascended to the status of a living God and Shinji absorbed inside it, Ritsuko unsuccessfully attempts to recover him.

Asuka sinks into deep depression after Arael's mental probing, and is unable to pilot when the new Angel Armisael arrives. Armisael begins physically fusing with EVA-00 and threatens to do the same to EVA-01, prompting Rei to sacrifice herself to save Shinji, only to appear alive soon afterwards.

Too frightened to face Misato or Rei, Shinji runs away yet again, only to meet and strike a friendship with Kaworu Nagisa, the replacement pilot for EVA-02. Kaworu's openness and friendliness provide much-needed comfort for the disturbed Shinji. However, suspicions abound over Kaworu's incredible synchronization abilities.

Instrumentality continues. The focus is primarily on Shinji now, as he learns to accept the individual’s ability to shape their world, and how the self cannot exist without others to define it.