In the year 2015, an Angel returns to attack on Tokyo-3. Misato Katsuragi transports Shinji to the NERV base overseen by his estranged father, Gendo.

After piloting the Eva Unit 01, Shinji wakes up in the hospital with no memory of the battle. Feeling sorry for him, Misato lets him move in with her.

Word gets around school that Shinji is the Eva pilot; his classmate Toji resents him for it. An Angel appears and Shinji must pilot in combat again.

Stressed out following his last battle, Shinji runs away from home and meets Kensuke. After NERV brings him back in, Misato offers him a choice.

Unit 00's pilot Rei Ayanami appears to have recovered, but she has no friends, no records of her past, and no interest in getting to know Shinji.

As the Fifth Angel drills toward NERV, Misato leads Operation Vashima: All of Japan's power will be diverted to take out Ramiel with a positron rifle.

Ritsuko tells Shinji about the classified true cause of the Second Imapct. Then she and Misato attend the field test for an Eva competitor mecha.

Shinji and his friends accompany Misato to meet Eva Unit 02 and its pilot Asuka at sea. Misato's old friend Ryoji Kaji is aboard with his own agenda.

Asuka and Shinji face another Angel but it gets the upper hand. They now have six days to learn synchronized moves to destroy it completely.

NERV learns of an Angel in dormant embryonic form inside a volcano. Using equipment designed for magma, Asuka is sent to retrieve it with Unit 02.

Tokyo-3 loses power just as another Angel is detected. The Eva pilots must enter the base from the surface while NERV preps the Units manually.

With Gendo and Fuyutsuki in Antarctica, a newly promoted Misato is in charge when a new Angel appears about the Earth, aiming to bomb Tokyo-3.

An Angel infiltrates NERV, quickly taking over the MAGI supercomputer, Ritsuko proposes writing a program to forcibly evolve Ireul to its extinction.

As Seele reviews NERV and Gendo's actions with the Third through Eleventh Angels, Ritsuko conducts a test in which the Eva pilots switch Units.

For the first time in years, Shinji meets his father at his mother's grave. Ritsuko, Misato and Ryoji attend a wedding and Asuka goes on a date.

While in battle, Shinji and Unit 01 are engulfed in the spreading shadow of an Angel. As NERV fears them both lost, Shinji has a strange experience.

NERV-02 in Nevada vanishes, along with the Eva Unit 04. With Unit 03 on the way, Gendo orders Ritsuko to assign a pilot to it.

Unit 03 arrives from the United States, but Shinji still doesn't know who its pilot is. During testing, NERV learns Unit 03 is possessed by an Angel.

Distraught after the battle, Shinji vows to never pilot an Eva again and quits NERV once more. Just as he's about to leave, another Angel attacks.

After achieving an unheard of synchronization rate, Shinji merges with Unit 01. While he has an out of body experience, NERV works to salvage him.

Seele kidnaps Fuyutsuki and interrogates him about NERV and Gendo's true intentions, revealing events from the past. Ryoji goes missing.

Asuka's synchronization ratio continues to drop, undermining her self-confidence. Determined to show her worth, she ignores orders during battle.

Despite her struggles, Asuka is ordered to assist Rei in battle against Armisael. When she fails, Rei makes a desperate move in order to save Shinji.

Kaworu Nagisa, the Fifth Child, comes to NERV to pilot Unit 02 in Asuka's place. He's friendly to Shinji, but he's shrouded in mystery.

The Human Instrumentality Project begins, and the souls of humanity merge. The Eva pilots confront the nature of their existence as reality dissolves.

The Human Instrumentality Project continues. Shinji must decide whether to accept a world alone, or embrace connections with others.