Continuing from the previous episode, the Angel Ramiel is drilling down into the GeoFront to attack NERV HQ directly. After Shinji barely survived a direct confrontation with it, Misato devises a plan to have EVA-00 and EVA-01 defeat the Angel by sniping it from a distance using a positronic rifle which requires the total electric output of Japan to power up.

Ritsuko briefs Shinji on the real nature of Second Impact, the Angels, and the Evangelions' mission to defeat them. Misato and Ritsuko attend the public demonstration of a new Angel-fighting robot, Jet Alone, built by a rival defense contractor to NERV. However, the nuclear-powered robot quickly runs out of control, and Shinji must use EVA Unit 01 to load Misato onto Jet Alone so she can she can enter in its automatic shutdown code, before it melts down in a nuclear explosion.

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.

The EVA pilots are disappointed to find out that they are not allowed to go on their class trip to Okinawa, because they have to stay at Tokyo-3 to stay on-call in case of an Angel attack. Meanwhile, a new Angel is discovered in a chrysalis-like developmental stage deep within the magma of the volcano Mount Asama.

Tokyo-3 comes to a standstill when sabotage knocks out all power, and the personnel must scramble to launch the EVAs manually when an Angel appears in the middle of the blackout.

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.

A routine test involving the EVA pilots turns into a struggle for survival when a wholly new type of Angel appears and spreads inside NERV HQ. This new, computer-like angel threatens to set off the self-destruct for the entire facility, leaving Dr. Ritsuko Akagi in a race against time to save the GeoFront and destroy the Angel.

In the first half of the episode, a clip show is presented to the Human Instrumentality Committee of Seele, reviewing the attacks of all Angels up to this point. The second part includes a poem in which Rei contemplates her own existence, and a cross-compatibility test between Rei's and Shinji's EVAs.

A NERV branch in Nevada is obliterated in a catastrophic accident, and NERV headquarters prepares to station a new Evangelion in Japan. The Fourth Child is selected, unbeknownst to Shinji.

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.

Enraged over Touji's near-death at the hands of his own EVA, Shinji refuses to pilot an Evangelion again and prepares to leave Tokyo-3 for good. He is forced to reconsider that decision when an immensely destructive new Angel attacks just as he is about to leave...

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'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.

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.