Godzilla X Neon Genesis Evangelion is set in an Alternate Universe of Evangelion 2.22 where NERV rediscovers Godzilla, who is now an enemy of mankind, but none the less is determined to destroy the Angels in the name of restoring balance.
- Godzilla - The main protagonist of the series, After the Second Impact Godzilla has lost all hope for humanity due to it's use of destructive weapons. He also remembered all the bloodshed and near extinctions he and the Angels had cause in their first war, but they two factions decided to make peace as Godzilla wasn’t willing to kill the planet to defeat the visitors. As such Godzilla had an uneasy alliance with the Adams, Lilith and, a few million years later, homo sapiens/lilin. But Second Impact was the last straw to break that alliance. The two races drew first blood, and now Godzilla will avenge the Earth.
- Shinji Ikari - In contrast with his role in the Mainstream Evangalion universe, Shinji serves as the deuteragonist rather than the protagonist (As that role was given to Godzilla).
- Rei Ayanami - The tritagonist of the series. Unlike the Evangalion anime and films, Rei takes Asuka's role as Shinji's primary love interest. After her and Asuka's defeat at the hands of Godzilla, Rei became terrified of the monster.
- Asuka Shikinami Langley - Asuka's role in the story closely mirrors that of the Rebuild of Evangalion films. She developed a strong obsession to kill Godzilla after denying a kill on an Angel by blasting it with his Atomic breath and later humiliating her in the ocean when she and Rei were tasked with finding the creature.
(More to come)