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.

Shinji begins attending his new school in Tokyo-3, and has a difficult time dealing with the fame of being an Evangelion pilot. Touji Suzuhara, who's little sister was injured in Shinji's fight against the Angel, is angry at Shinji. A new Angel appears, and Shinji must once again pilot EVA-01 to defeat it.

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"...

Misato has been promoted to Major, but the celebration does not last long. A monstrous Angel appears in Earth orbit right when Gendo and Fuyutsuki are away, leaving her and the children to deal with a colossal kamikaze threatening to drop itself right on top of Tokyo-3.

Shinji beats Asuka in a synch test, much to her annoyance. Not too long after, the EVAs are dispatched to deal with a mysterious apparition, and EVA-01 is sucked into a shadowlike blackness that materializes out of nothingness from under it. While an emergency operation to rescue the captured EVA is concocted, Shinji goes on a trip into the depths of his own consciousness...

Evangelion Unit-03 arrives from the United States. However, its activation experiment brings out NERV's worst nightmare when it turns out to have been infected by the Thirteenth Angel. The other EVAs are dispatched to battle the Angel-infected abomination... even at the risk of killing its helpless pilot.

Asuka's synch rate is on a downward spiral after her defeat at the hands of the Fourteenth Angel, Zeruel, and her frustration with Rei, Shinji, Misato and Ryouji is on the rise. Angrier and more disturbed than ever, she is forced to relive her dark, traumatic past during the encounter with the Fifteenth Angel, Arael.

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 has begun, and now its inner process, the joining of all souls into one, will be depicted. The episode is primarily driven by dialogue, the background usually complete darkness. White text often appears on a black screen, an omniscient voice questioning the characters.

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.