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 is upset with Shinji for ignoring her orders in the last Angel battle, and he is so overcome by the stress of being an EVA pilot that he runs away. After wandering around Tokyo-3 for several days, Shinji is faced with the choice of quitting or staying in his new home.

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.

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.

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.