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Fifteen years after the "Second Impact" devastated half the planet, the survivors are scattered and struggling to live normal lives. Everyday, they live in fear of the beings known only as "Angels," which appear without warning and are virtually indestructible, with their "AT" (Absolute Terror) fields. In Tokyo 3, the international NERV agency has developed a new weapon made to battle the alien giants. It is called "Evangelion," and it is a techologically advanced fighting machine that connects with the nervous system of its pilot, making movement and commands very easy to control. However, the EVAs are extremely unstable and can only be piloted by children born 9 months after the 2nd Impact.

Shinji Ikari is one of three children chosen to be EVA pilots. His father Gendo is the cold, enigmatic commander of NERV and rarely even acknowledges his son's existence. Another chosen pilot is Asuka Langley Soryuu, a confident, arrogant girl who is Shinji's complete opposite. The last child is Rei Ayanami, who is even more silent and odd than Shinji. She seems to have a mysterious connection to Gendo and the secrets of NERV. Together, they must fight against the deadly Angels with little or no information to help them and at the same time, keep control over their volatile EVAs and the memories of their tragic childhoods.

While their world is destroyed around them, the pilots of the EVAs and the members of NERV still must deal with their complex relationships and their internal conflicts with the true purpose of their organization. They begin to question their beliefs and their positions as pawns in NERV's master plan. Old friends hide secrets and conspire with the enemy, while the ignorant simply try to survive another day.

As the Angels arrive one after another, the horrifying origins of the EVAs are revealed, as well as the reason for the Angels' attack. They begin to develop defenses against the EVAs' weapons, forcing the pilots to improve their fighting and tactical skills or die. From physical damage to Tokyo 3, the Angels' method of attack moves to mental harm to the pilots of the EVAs. Caught by surprise, one pilot is forced to relive traumatic memories and another is forced to feel emotion for the first time before committing the ultimate sacrifice. These two attacks are only a precursor to the final Angel's arrival, an event heralding the end of humanity.

Ultimately, it is Shinji who must decide mankind's fate. His battle to overcome his self-hatred and apathy proves to be humanity's last chance. Despite all the battles won and the lies revealed, despite the struggles overcome and the sacrifices made, the Third Impact finally comes, and it is unlike anything that was ever expected.