In my humble opinion, Neon Genesis Evangelion is one, if not the, best anime of all time. It is certainly one of the best stories ever told, but also one of the deepest and most confusing. So, what follows is purely my understanding of some of the more unclear and mysterious parts of the story. Be warned: there will definately be spoilers.

In the beginning of the story, we are introduced to AT (or Absolute Terror) fields: fields which both angels and Evas alike can use as a barrier from damage. Though this is true, it is very far from the complete definition of an AT field. In episode 24, Kaworu reveals to Shinji that all living things have an AT field. It is the thing that keeps your ego as you, for without the AT fields, there would be no boundaries between anyone, and all life forms would merge together as one. In earlier episodes, it is revealed that Evangelions are not giant robots, but the spawn of Adam, the first angel (or in the case of Eva Unit 1, Lilith, the second angel) contained in an armor that keeps them under the pilot's control, though over the series, we see them take control quite a few times, like the first time Shinja pilots Unit 1, and during Rei's test in which Unit 0 tries to attack Gendo Ikari, Shinji's father. The goal of Seele and Nerv's home-brewed Third Impact has very much to do with AT fields.

Second Impact happened in Antarctica, where an experiment went wrong, resulting in the destruction of half of the world's population. Though it was covered up, what caused it was Adam's contact with the Lance of Longinus: a lance with the ability to destroy AT fields. The research team was trying to turn change their newfound God into an embryonic form, so that they could take it and use it. This went wrong, and the Second Impact heppened. In episode 8, Kaji delivers the embryonic Adam to Gendou; it will live inside his hand for the rest of the series. In the series, the Lance is stuck through Lilith, who everyone but Gendo Ikari, Ritsuko Akagi, and Seele believe to be Adam, on a cross inside central dogma, which would keep her there and under control until Seele needed her. Gendo Ikari, along with Seele, was working at the site of Second Impact up until the very day before it actually occured. How did they know to get out? They found the Dead Sea Scrolls: scrolls with premonitions of the future, such as the coming of the angels, and obviously, the occurance of Second Impact. With the Dead Sea Scrolls in their hands, Seele was able to very intelligently manipulate people and organizations to achieve their goal: the Human Instrumentality Project and Third Impact.

The Human Instrumentalit Project was created to fill a void that exists in everyone. That void is what makes us scared, or lonely, or hurt. In the series, we see pretty much every character we care about sink into a depression because of this void... loneliness. The goal of the Human Instrumentality was to fill the void with eachother; have every human filling every human's emptyness. But how can they do that? How can they get one awareness to enter another one? The answer is Third Impact. Third Impact, which would happen when Adam and Lilith join. Throughout the series, there is talk of man creating God by making the Evangelions. This is because they are exactly like Adam and Lilith, who, for all intents and purposes, are Gods. When they join, they will emit an enormous anti-AT field, which will break down the AT fields of every living being, reducing them all to just a consciousness in the form of primodial soup. Everyone would join together as they are pulled towards Lilith, and would all fill their voids. The world would be however they wanted, for everyone contains a multitude of truths for an instance, every single one of those truths would exist in everyone, and their own world experienced in their consciousness would be comprised of which ever they like. Though Gendo's wishes are the same, the details are slightly different (more on that in a bit). With his aim in mind, he does small things along the way to gain the upper hand, such as dispose of the lance of longinus, so that Adam could not be used in the Third Impact.

Yui Ikari, Shinji's mother and Gendo's wife, disapeared during the first activation of Eva Unity 1. She is presumed dead, but it is strongly hinted at that she chose to merge with Unit 1, so she could protect the people she loves, just like the reason she gives foor bringing Shinji to Gehirn's (Nerv's predecessor) headquarters. Right after that, Rei appears on the scene. Gendo introduces her as an "acquantances daughter," but she is actually a genetic clone of Yui. Gendo would use her, and her many clones, to bring himself closer to his goal. The Rei that is active in the world would be an Eva pilot, the clones would be used to fill the dummy-plugs, which allow the Eva to be active "without a pilot." In the end, he would also use her as a means of joining Adam and Lilith. In the movie, we see him reach into her breast, his hand disapearring into her body, so as to transfer Adam to her, and they could both join with Lilith. Remember the fight with the 17th angel? Why didn't Gendo want to take Unit 1 out of cryostasis to help fight? Because by keeping it locked up, there was no chance that it could replace him in the joining with Lilith. It's unclear what his decision would be for the rest of all life, but he personally could then emerge from Lilith's dark egg with Yui, and he would have achieved his goal. However, this third Rei isn't the same as the second. She looks at Gendo's glasses with contempt when the second kept them lovingly. At the last second, Rei pulls back. Gendo should not be the one to decide the future of all life. The one to do that should be...

Shinji's fight with the 14th angel, in which his Eva woke up and actually ate the angel, resulted in Eva Unit 1 gaining something called an S² engine, or Super Solenoid engine. This engine, or organ, is the Anegls' power source. It gives them an unlimited power supply. This makes sense, seeing as how they are living things, and shouldn't need to be plugged into something, like the Evas are, to function. Now that Eva Unit 1 has this, it has all of Adam and Liliths power, and no longer has the weaknesses of an Eva. For the same reasons as those for Adam and Lilith, it is now a God. In the movie End of Evangelion, we see Shinji taken into a strange world where his consciousness will decide tha future of life. That is because Eva Unit 1 has replaced Adam in this artificial Third Impact as a God.

The person who feels the void the most out of anyone in the series is definately Shinji. He spends most of his life alone, hating himself. The decision of changing all life as we know it into primordial soup, which in theory is a good thing, but in all honesty is downright horrifying, is left up to Shinji. Should he return the world in which he was lonely all the time, or continue into a frightening new world of uncertainty. As he struggles to decide, the world is already changing. In the last moments, Shinji decides, and he emerges as a human from within the sphere in which all consciousness is gathering. When everything has calmed down, we see that he brought Asuka with him. He chose to spend the rest of his life with her in this brand new world. The last words of the fiilm, spoken by Asuka, which can be translated from Japanese in a multitude of ways (I feel sick/this is gross/I don't feel well/this is disgusting/etc.) were spoken in English as "How disgusting." This was a poor choice, as it seems to give off a different meaning (that Shinji sickens her) than it was intended (that everything that has happened to her disoriented her).

This is my understanding of the story of Neon Genesis Evangelion, one of the greatest stories ever told.