Three years after Shinji Ikari prevented Third Impact during the Battle at NERV HQ, the Earth is at peace once more. NERV has been reorganized under the command of Misato Katsuragi, and Shinji leads the EVA team with the help of his friends Asuka Langley Souryuu and Rei Ayanami. Advancements in technology have led the organization to upgrade its Evangelions, and three Series-0.0 units have been placed into low Earth orbit to watch over the planet.

Just as NERV is on the verge of upgrading Shinji's Unit-01 Type-F, one of the Unit-0.0s goes out of control and crashes near Tokyo-3. Soon after, NERV is attacked by a mysterious Angel Carrier—an oddly modified Mass Production Evangelion. It is now up to Shinji, Asuka, and Rei to stop this attack and identify their mysterious new enemy.