The year is 2015, fifteen years ago the earth nearly came to an end when a meteor struck the Antarctic continent. Only half of the human race was left a year later. The Antarctic incident caused the earth's climate to change, raising the oceans by sixty meters submerging coastal regions forever. This meteor it seems was no accident, rather it was the work of the mysterious objects known as "Angels".

Their purpose in attacking earth originally is unknown yet the Angels have returned after fifteen years to attack Tokyo-3, a mechanised defense fortress. Underneath Tokyo-3 is the underground base known as NERV, a secret organisation under the shadow of the United Nations. Here the Evangelion units exist. There is a problem however with pilots for these units, only teenagers with special characteristics can synchronise with an Eva unit. As the story begins only three have been found through a search by the Marduk Institute, the third being Ikari Shinji, son of NERV's supreme commander Ikari Gendou.