In the year 2000, half the world's population perished in the collision of a meteor at the Antarctic, which became known as the Second Impact. This was what was known to the public. However, a few chosen knew the truth, that the Second Impact was caused by man's first contact with the entities known as Angels.

Being seriously hurt in the Second Impact, a special secret agency was set up directly under United Nations called NERV which for the studies and supposedly annihilates the "evil" Angels. They built their secret headquarters at Geofront, which is the underground of the fortress city Tokyo-3, the current city. After 15 years of work, a gargantuan humanoid fighting machine called Evangelion, or Eva, was developed which can fight against Angels. 

Presently, In the year 2015, Shinji Ikari is summoned by his apathetic father to Tokyo-3, where he encounters the return of the Angels and is told of his role in helping the secret organization NERV save the human race. He must pilot the mighty Eva-01 into battle to defend the earth against the Angels.

Now this young boy, who cares for little, including himself, must find the courage to face what could be the greatest threat mankind has ever faced. Will he be up to the challenge? What is behind the Angel attack. And even if he manages to defeat the Angels, is that where it will all end?