The government's fears come true and another angel attacks, but Tokyo-3's first Eva unit & child (Eva-00 & Rei Ayanami) were damaged in a testing accident, so they need a pilot in a hurry. The man in charge of the operation, Gendo Ikari, summons the son he abondedend as a child, Shinji Ikari, to NERV's headquarters. Given little explanation, Shinji is instructed to try to synch with Eva Unit 1 (Eva-01) to fight the angel. Furious that's the only reason his father summoned him, and confused and scared about the whole idea, Shinji refuses until he sees how badly hurt the only other pilot available, Rei, is. Shinji surprisingly is able to synch with his Eva unit quickly and seems to synch too much with it when he blacks out and can't remember how his Eva went berserk and killed the angel.

The problem now is that angels are coming closer and closer together than before. (The first break was 15 years, now they come days apart.) Rei joins back in the action after a few episodes, and Asuka Soryu Langley, among other children also join the fight. Meanwhile, Shinji's father shows no affection for his son and Shinji instead rooms with Misato, the head of operations of the Evas, forming a deep friendship with her. The story starts off fairly light with a destroy of humans fighting invaders with quite a bit of comic relief, but soon evolves into a bit darker as the truth behind NERV and its founders is sought. What really happened to cause the Second Impact? Who, or what, are the angels? Are they really our enemies?…

Shinji Ikari Shinji Ikari is the protagonist of the story. His mother died when he was young, and his father sent him away so he would not have to deal with him. At age 14, he is called to meet his father, and in hopes his dad might apologize for forgetting him, he goes to see him. It turns out his father only needed him because he has the ability to pilot an Eva, and with little explanation and no training, he fights an Angel and somehow succeeds. He makes a great friend in Misato, who takes him in to her apartment, rather than having him live alone on base. Rei Ayanami Rei is the mysterious, almost surreal "first child." Not much is revealed about her origins until the end of the series and the movie, but even then not every question is answered. At the start of the series, she is being treated for injuries that occurred to her during an accident with her Eva. She seems insensitive to what goes on around her, and her only friend is Gendo Ikari, Shinji's father, who treats her better than he does his own son. Throughout the show, Shinji tries to befriend her, but Rei is only interested in her piloting duties, in which she pilots Eva unit 0-0.

Asuka Soryu Langley A half-Japanese, half-German girl, Asuka, the "third child," was raised in Germany which is where her unit, Eva 0-2, came from. Asuka starts off as an obnoxious girl who is proud to be an Eva pilot and thinks she does a better job at it than Shinji or Rei. She sometimes lets this vanity get to her head and goes against orders to fight how she thinks would be correct. Towards the end of the show, however, we learn of Asuka's reasons for wanting to pilot an Eva, and the sad past she is haunted with.