After the impact, only half of the human race was left a year later. The object that had crashed into Antarctica was a gigantic, living organism. It stayed inactive for a brief period of time.

Humans' curiosity got the better of them, and they to search for the object. During the search, the object self-destructed and blew Antarctica to bits. The heat given off by the explosion was so intense that the ice of the entire continent melted, provoking floods, raising the oceans by sixty meters; submerging the coastal regions forever. It also destroyed biblical proportions of the surface of the planet. Only a handful of living things managed to survive. The Angels also warned that they would leave the Earth untouched for another fifteen years so as to serve as a chance for the human race to "learn" from their mistakes.

Humans, not knowing what they had done wrong did nothing but start to develop a secret organisation under the shadow of the United Nations, called NERV. It was given unlimited funds in for research and development of new weapons to fight against the Angels. Of all the weapons developed, only the Humanoid Final Battle Weapon, code named EVANGELION(EVA.), giant cyborgs which were the fruit of the Angel technology captured fifteen years ago, was the only thing powerful enough to defeat the Angels.

Tokyo-3, an underground city used to protect the citizens, was also built. At the lowest level of the Tokyo-3, is where NERV is situated.

Indeed fifteen years later, AD 2015, the Angels did return. Each time they attack, they seem to know the exact location of the NERV base, and try to destroy it. Fortunately, Evangelion units are powerful enough to hold up to the Angels. However there is a problem, only teenagers with special characteristics can synchronise with an Eva unit.

Commander Ikari of NERV, director of the mysterious "Human Aid Project", established a program code in AD 2001 called, "Marduke". The purpose of this program was to find suitable pilots for the Evangelions. To date (2015 A.D), that program has only yielded three pilots, all of them 14 years old: Rei Ayanami , Soryu Asuka Langley and Shinji Ikari, Commander Ikari's son.