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Tomoya is labelled as a delinquent at his school because he is constantly late and skips classes, but he seems to have little care about how others perceive of him. Everything in his life seemed dull and unchanging until one morning he meets Nagisa Furukawa on the road to his school; he finds her muttering to herself to give her more motivation for the school day.

The city of Tokyo has been overthrown, taken over by Invaders who have devastated the rest of the planet. For 15 years, the remnants of the human race have fought a losing battle against the Mu and their Dolem, knowing that the key to victory lies within the domed walls of Tokyo Jupiter, where time flows in a different path and none of the mind-wiped citizens even know that the city has been conquered.

Aizawa Yuichi had often visited his cousin in the city when a young child. However, something drastic happened to keep him away for seven long years.

In 2015 huge, tremendously powerful alien war machines return to Tokyo. The only hope for Mankind's survival lies in the Evangelion, a humanoid fighting machine developed by NERV, a special United Nations agency.

Events in After Story take place immediately after the end of the first part, but extends into the next ten years, where Tomoya and Nagisa live together as a family. Life continues on for Tomoya.