The story begins in the year 2000 (at the time of the series, this was considered in the future).  Humans found an entity in Antartica, which turned out to be Adam, the first angel.  A scientific research team was sent to Antartica and tried to shrink Adam.  This backfired and caused a poison flood that drowned over half the human population.  Gendou Ikari left Antartica two days before this Second Impact. In the aftermath, NERV was formed and the remaining human population were told that the impact was a result of a comet hitting Antartica and melting the polar ice caps.  NERV built a fortress that's called Tokyo-3 and was guided by predictions found in the Dead Sea Scrolls, which predicted the arrival of the angels and humanity must defeat them all to achieve human completion.  Gendou's wife, Yui, originally theorised the possibility of creating Evangelions and was the first test pilot.  She died of these experiments.  It is said that her soul was left in EVA-01.  After her death, Gendou became very cold and withdrawn and began taking care of a little girl named Rei Ayanami.  Naoko, a scientist, became romantically involved with Gendou and jealous of Rei.  She killed Rei then committed suicide, but no one ever found out about this. For some reason, it was determined that only certain children born after the Second Impact could pilot evas.  They must be 14, have no parents and be psychologically disturbed.  By 2015, the tv series begins with the appearance of angel 3 and the arrival of Shinji to Tokyo-3.  Tokyo-3 is attacked by 17 angels, no two of which were remotely similar to each other.  When Kaji and Asuka arrives, Kaji brings with him Adam in his embroic form.  It is Adam who is used as a genetic donor of Eva body matter.  Asuka is the second child and her sych ratio is initially the highest of the pilots.  But Shinji has more natural ability and quickly catches up and surpasses her.  Rei saves her life and Asuka believes she is in third place, which causes her to develop depression.  The battle with the 15th angel is her last chance.  She fails and runs away but is found lying naked in an empty bathtub in some crumbling apartment.  She is put in protective custody.  NERV develops a dummy plug system, which is described as a machine that duplicates Rei's thought signals to an eva.  Rei sacrifices herself to save Shinji in the battle with the 16th angel and her eva explodes.  She survives, however, and tells everyone that she is the third one.  Meanwhile Ritsuko is anticipating Misato's suspicions of NERV and takes Misato and Shinji to the eva graveyard.  This is the place that contained skeletons from failed experiments.  She revealed that Rei is a clone.  The tank of clones is the basis for the dummy plug system.  Ritsuko reveals that three Reis of been released into the world then turns off the life support for the clones and is arrested by NERV.  The 17th angel appears in the form of Karou Nagisa as the new Eva-02 pilot.  He believes that Adam is kept underground, but when he finds that it's the 2nd angel Lilith instead, he convinces Shinji to kill him.  The final two episodes represent the long awaited Human Completion.  They are montages of the characters exploring their personalities.  The series ends with Shinji accepting who he is and everyone in his mind congradulating him.