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.

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.

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.

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.

Kouzou Fuyutsuki is kidnapped and interrogated by Seele, who are horrified over the results of the last encounter with an Angel. He recounts his past, providing flashbacks into the creation of Nerv. The pasts of Misato Katsuragi, Ritsuko Akagi, Rei Ayanami and Yui Ikari are also revealed. Ryouji Kaji, meanwhile, decides to find out the truth, no matter the cost.

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.

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.