In the year 2000, humans found some sort of entity in Antarctica. This entity was Adam, the first Angel. A scientific research team, including Gendou Ikari and the scientist father of Misato Katsuragi, tried to shrink Adam to his embroic form. However, a tremendous explosion resulted from their work. The cause of the explosion was that even though they managed to shrink Adam, they weren't able to shrink the energy released along with him. Thus, this turned Antarctica into an ocean of poison and drowned over half of the human population. Strangely, Gendou left for Japan the day before the Second Impact occured, carrying much of the data that they had so far collected. Misato's father saved her by placing her in a floating escape pod.
In the aftermath of the Second Impact, a secret committee, called SEELE, created NERV. NERV is the United Nations Military agency dedicated to the Human Instrumentality Project. The reasons behind the Second Impact were hidden from the world, and instead, people were told a lie. The world was told that the Second Impact had resulted from a comet hitting Antarctica, thus melting the polar icecaps.
NERV was build in the Geofront, a perfectly spherical cyst-like cavern discovered under Japan. On the surface, the fortress city of Tokyo-3 was built. The skyscrapers of this city were designed to retract into the ground, becoming suspended from the roof of the Geofront. This is so they will not be damaged from the fighting above.
Gendou Ikari and Kouzou Fuyutski were made Commanders of NERV. It is interesting to note that the SEELE commitee is guided by predictions found in the Dead Sea Scrolls. The Scrolls predicted the arrival of the Angels and that humanity must defeat them all in order to achieve Human Completion.
Gendou's wife, Yui Ikari, was a brilliant scientist and gave birth to a son, Shinji Ikari, less than a year after the Second Impact. It was Yui who originally theorised the possiblity of creating Evangelions and was the first test pilot. Evangelions are huge artificial biological organisms engineered from tissue collected from Adam. They apparently have some form of rudimentary mind but no soul or willpower of their own. These elements are provided by human pilots. The "entry plug" is inserted into back of the Evangelion, containing the pilot, which will control the Eva. An Evangelion (or Eva), like an Angel, can generate an A.T. (Absulute Terror) field, making it close to invulnerable. The Eva's are covered in a metal armour which is intended for restrain and controlling the beast inside. An Eva requires electricity to move and its internal battery will drain in five minutes after activation, thus immobilizing the creature.
Yui died as a result of her experiments. There is a strong implication that while she was attempting to synchronize with Eva Unit-01 and lost her soul as a result. Thus, her body liquified and she vanished. Her soul is said to occupy EVA-01's Main Core. Shinji, aged 4, saw his mother die, but he suppressed the memory and totally forgot about it.
After Yui's death, Gendou became cold and withdrawn. He left his son to a private tutor in Tokyo-1 and ignored him for the next ten years. Also, Gendou became involved with Dr. Naoko Akagi. Naoko was the leading computer engineer of NERV and designed the Super Computer Magi. It seems like Gendou was involved with Naoko only because he wanted her to finish her work on the Magi system. Naoko introduced her daughter Ritsuko, then a college student, to Misato.
Misato, who had not spoken a word since the Second Impact, had begun talking again. Misato went out with a guy named Ryoji Kaji and became very close to him. She apparently cut a whole week of college just to have sex with him constantly. Ritsuko considered this disgusting and believed that there was a diffrent side to Misato that she didn't know about. Misato, Kaji and Ritsuko all become good friends and all later joined NERV in different departments.
The super computer Magi, which Naoko designed, consists of artificial organic brains supplemented by electronic circuitry. The Magi are composed of three parts, each named after the three wise men of the East (New Testament). They are called Balthasar, Melchior and Casper. The core programming of each processor was a separate replicated portion of the Naoko's own p ersonality. The Magi replicated her as a mother, her as a scientist, and her as a woman.
A short time after Yui's death, Gendou began taking care of a little girl called Rei Ayanami, claiming she was an acquaintance's daughter whom he was acting a guardian for. Rei looked a lot like a child version of Yui except that Rei had blue hair, red pupils, and pale skin. One night, Rei got lost in Central Dogma (the center of NERV) when Naoko was there alone. Rei started naming Naoko an "old hag". When Naoko said that Gendou will punish her for sayings things like that, Rei responded that she was just repeating what Gendou always called her to Rei. Naoko, knowing that this was the truth, strangled Rei in a fit of rage. When she found out that she had killed Rei, she commited suicide. Strangely, the events were completely covered up. Nobody knew of Rei's death or the reason for Naoko's.
For some reason, it was determined that only certain children born after the Second Impact could pilot Evangelions. These childern are chosen by the Marduk Institute. It is later revealed that there is no Marduk Institute. Instead, NERV is pulling all the strings. So, what does it take to be an Eva pilot? No one knows. It wasn't explained very well in the TV series or in the movies. From what the TV series layed out, you have to be 14, have no mother/father and be psychologically disturbed. All of the Eva pilots in the TV series were mentally unstable (except for Touji Suzuhara, but he wasn't a "true" Eva pilot and nearly died because of this).
By 2015, Ritsuko had taken over her mother's place as chief technical engineer for NERV and as Gendou's lover. Misato had long since broken up with Kaji, and had become NERV's chief tactical officer. The TV series began with the predicted appearance of the third Angel, Sachiel, and the arrival of Shinji in Tokyo-3. Upon arriving in Tokyo-3 during the Third Angel's attack, Shinji was taken down to the GeoFront and was told that only he can defeat the third Angel by activating EVA-01.
Throughout the TV series, Tokyo-3 became assaulted by seventeen Angels, no two of which were remotely similar to each except for their ability to create an A.T. field. This field worked as a defensive shield making the Angel close to invulnerable to any form of conventional attack. A.T. fields can only be neutralised by: another A.T. field (one generated by an Eva), incredibly powerful energy weapons (Positron Rifles), the Progressive knife or by the Lance of Longinus. The Lance is a huge metal spear of unknown origin. It is believed that when Commander Ikari and Fuyutski left Tokyo-3 together and went to the south pole, they retrieved the Lance from there. In the Bible, the Lance of Longlinus is the Lance which speared Jesus Christ. The one brough to Terminal Dogma is a larger version which was no doubt found together with Adam when he appeared in Antartica. It is this Lance that impales Lilith and stops her from regenerating.
When Kaji and Asuka joined up with NERV in Tokyo-3, Kaji brought with him a suitcase containing Adam in his embroic form. It is Adam who is used as a genetic donor of Evangelion body matter. EVA-01 is cloned not from Adam, but from Lilith, making it unique.
Adam was apparently installed in Terminal Dogma, a vault at the bottom of the NERV underground headquarters. This is supposed to be the safest place on Earth. We are originally led to believe that the being in central Dogma is Adam. This is ,however, untrue. The crucified being is actually Lilith, the second Angel. It's interesting to note that L.C.L is Lilith's blood.
Asuka Langley Sohryu, the Second Child, is the pilot of EVA-02. Her synch ratio, the measure of a pilot's ability to control an Evangelion, was initially the highest of the three pilots. Unfortunately, Shinji appeared to have a greater natural ability and quickly caught up to her. Shinji eventually surpassed Asuka, and this hurt her tremedously. It went from bad to worse when Rei saved Asuka's life, putting Asuka into third place in her own mind. Asuka went into depression and attempted to dominate her Eva instead of merging with it. Thus, her synch ratio and mental state, became progressively worse.
NERV developed a "dummy plug" system in an effort to activate and operate an Eva via computer. The specifics of the system were not originally revealed, but the dummy plug was described as just a machine which duplicates Rei's thought signals to an Eva. However, unlike Rei, the dummy plugs had no soul.
The Lance of Longinus was removed from the Lilith's chest by Rei in order to kill the 15th Angel. The Angel attacked Tokyo-3 from orbit around the earth and was outside of any weapon's range. EVA-00 threw the Lance at the Angel and the 15th Angel was destroyed. Unfourtunatelly, the Lance could not be retrieved from orbit. The 15th Angel also destroyed the last vestiges of Asuka's ability to synchronize with an Eva. The battle against the 15th Angel was Asuka's last chance to redeem herself as a pilot. After her defeat, she was dicharged from NERV and promptly suffered a massive nervous breakdown and lapsed into deep depression. After disappearing, she was found by NERV inteligence lying naked in an empty bathtub in some crumbling apartment block. After this incident, she was put under protective custody by NERV.
The 16th Angel, which appeared as a giant circle made from a double helix, attacked EVA-00 and integrated itself into the Eva's biological matter. With contamination levels going throught the roof, Rei was ordered to eject. But, for what was apparently the first time, she disobeyed the order and made her Eva core go into "critical mass". The result of this was that Unit-00 exploded, destroying most of Tokyo-3. The reason she gave for sacrificing herself was that she wanted Shinji to be safe. Her shattered entry plug was found, but what was left inside of the plug was classifed as "top secret". Miraculously, Rei did not die of the blast. She was heavily bandaged and had no recollection of the events that happened. She tells us that she was the "third one". What she is refering to is that this is her third body.
Misato, finally understanding that there is more to NERV than her superiors let on, asked Kaji for information. Kaji, himself a spy for the Japanese government and for SEELE, showed Lilith to her. Misato also seduced Kaji in order for him to tell her more. Kaji gave her a capsule, containing a data chip, which contained the answers to all her questions, and more. Unfourtunatelly, its contents is never revealed in the TV series.
Shortly thereafter, SEELE gave Kaji orders to kidnap Commander Fuyutski and bring him to them. The Commander was then questioned about Commander Ikari's intentions and goals. After Kaji released Fuyutski, he was shot by an unknown gunman. Misato, who had been suspended from duty due to her relationship with Kaji, was given back her gun and security card. She was told that "everything has been taken care of".
Ritsuko, anticipating that Misato would try to force information from her, arranged for Shinji to be present when she entered a restricted area in Central Dogma. Ritsuko, like her mother, was disillusioned with her relationship with Gendou and was having a severe personal crisis. She showed Misato and Shinji the "Eva Graveyard", which contained skeletons from failed experiments. She also told Shinji that he saw his mother die. Ritsuko finally revealed the secret about Rei: a tank full of identical Rei clones. These, it turned out, were the basis for the dummy plug system. Each dummy plug contained a soul less clone. Apparently, three of these clones had been successively released as the living Rei Ayanami. Strangely, only one clone at a time can have a soul. The first Rei was strangled by Naoko, the second sacrificed herself and the third is currently "alive".
We find out that Ritsuko hated Rei immensly and turns off the life support for the clone-tank, killing all the remaining clones. Ritsuko believed what she did wasn't murder because the clones did not have souls. Only the third Rei survived of all the clones. Ritsuko was removed from duty and locked up in prison by NERV.
The 17th Angel appeared in the form of a boy called Kowaru Nagisa. He resembled Shinji, except for the fact that he had grey hair. Like Rei, he had pale skin and red pupils. Kowaru was sent by SEELE as a the new EVA-02 pilot. Shinji became friends with Kowaru, who shortly thereafter told Shinji that he loved him. Shinji, desperate for human contact and warmth, opened up to Kaworu and loved him back. Not long after that, Kowaru activated EVA-02 (without even getting into it), generated the most powerful A.T. field on record, crashed through all the barriers leading to Terminal Dogma, kept EVA-01 and a confused Shinji busy with EVA-02 and opened Heaven's Gate, the acces door to Terminal Dogma, by glancing at the lock.
Strangely, Kowaru stopped just short of making contact with Lilith. Before him was not Adam, instead it was Lilith. He has been fooled by the "Lilim". He told Shinji that only one being could survive the annihilation and although Kowaru was himself immortal, it need not be him. He declared that he preferred the freedom of death over the burden of eternal life and told Shinji that he is the one who needed a future. He asked Shinji to kill him, and the saddened Shinji did.
However, the final two episodes of the series were hard to interpret. They were supposed to represent the long awaited Human Completion, but were presented in a surrealistic fashion. For any casual viewer, they would have seemed like a mish-mash of sequences, which were all recycled, containing constant talking about nothing. Those people would in fact be right, as that's all episodes 25 and 26 were. It is in these two episodes that the Third Impact had occured and that is why all of the characters were talking about nothing. Then why is it done so badly, you ask? Didn't you know that Project Eva ran out of money at this time?
The actual episoded consisted of montages exploring the character and their personalities. We all got a look how Misato, Asuka, Rei and Shinji existed within each other's mind. Although all four have very different personalities, they are all shown to be acting out of their need for contact with other. The series ended with Shinji accepting who he is. He is then congratulated by the other characters who existed within his (mentally unstable?) mind.