The best way for me to understand Evangelion is to collect all of the information learned throughout the entire series and End of Evangelion, then putting all of the information into a rough chronology. Essentially looking at the events from Seele's viewpoint, instead of the main characters'. My purpose is to make sense what happens to Shinji and Asuka by the end of the movie. Their are still many elements of the series that I do not fully understand.
This Interpretation is heavily based on the ones written by the officers of the Cornell Japanese Animation Society (CJAS). You can read the articles at their website. This interpretation is actually only a fleshing out of what they have already done.
If you need to refresh your memory of the series, you can read the scripts at Charles Kwong's Neon Genesis Evangelion Page
In the beginning humans and the possible alternate dominate lifeforms, Angels, were created. Adam mated with Lilith and they became the parents of humanity. I think of the Evangelion setting as an alternate world, where the descendents of Adam and Lilith became more distant from one another than humans in our world.
Centuries later, Christ was slain and a man spat on his grave. He was cursed to become the Wandering Jew and later was known as Keel; he is one of member of Seele. A CJAS officer put forth this idea to explain how the people who caused the Second Impact assembled the artifacts for the ritual.
By 2000 A.D., human had interpreted the Dead Sea Scrolls and under Keel's guidance, began the Instrumentaliy of Humanity Project (also called the Human Complement Project). This project was to save humanity from the pain caused by the fundamental distance between them. This was the hedgehog's dilemma, where Shinji could not close the distance with anyone else because he did not want to get hurt. In the Evangelion setting, that distance existed between everyone. Shinji felt more strongly than everyone else, because he completely lacked confidence in himself and fell flat on his face trying to lean on other who were distant from him. The project would give Keel a repreive from wandering the Earth, because his sin would be expiated. Humans began the ritual and began the events fortold in the Dead Sea Scrolls. Humanity would have to overcome challenges, which would come in the form as Angels. The Angels would come to try to meet Lilith, to initiated their own version of the Third Impact to remake Earth for themselves.
At the beginning of End of Evangelion, human have met these challenges and the stage is set for Seele to force the Third Impact to obey Keel's image. The purpose of the brutal assault by Seele was to take control of the Evas 01 and 02. Unit 01 was needed to initiate the Third Impact and Seele needed to control Unit 01 to control the outcome of the Third Impact. Angels could initiate the Third Impact for two reasons; they had S2 organs and some form of a soul. Units 02 didn't have a S2 and the X2 series Evas lacked souls.
Asuka tried to prevent the ritual by destroying the X2 series, who could only die if the red spheres, which I assume hold the S2 organs were smashed. Without taking out the S2 organs, the mass production Evas arose with massive injuries to tear Unit 02 to pieces. At the end of the movie, Asuka's arm and eye are wounded, which means that she passed out and lost her link with Unit 02 after Asuka felt her arm get split in half (along its length).
After Asuka is defeated and Shinji's will is broken down, the Third Impact begins. Eva is assimilated with the various artifacts and symbols becomes the Tree of Life and basically everything in one. I interpret the figures being drawn into black sphere that Lilith forms as the physical lifeforce and thoughts of the human and the crosses left behind on earth are the souls. Since the human souls are on Earth, the process still can be reversed. Shinji is at the center of the Third Impact, so he can decide a part of the ritual's outcome.
Without their AT fields human cannot maintain their forms and become one in body as a pool of LCL and one in mind in the center of the impact. Without a world, a body, and possibly a future as we know it, Shinji looks within. The minds of the characters seem to brush each other as all of their minds come into contact.
At one point Shinji attacks Asuka after he asks her for help. She has an emotionless stare and doesn't react much when he strangles her. She hangs limply like a doll in Shinji's grasp. His explosion of anger is a honest reaction and starts him on the path to digging deeper within himself.
Eventually, he sees his mother and feels her emotions for him. I believe in that moment he feels loved and complete and that he can try to find that feeling alive with others. That's why he gives the world that he knew, replete with AT field, another chance. He wants to make his own choices and live, this is his choice to grow up. This is inspite of his knowledge that such feeling and perhaps even the revelation that he people don't hate him because he is Ikari Shinji are like "a prayer that cannot last". When he returns, all other human can return if they wish. Practically everyone chooses to ascend into the new union of souls that is one step closer to Heaven.
One person chooses to return, Asuka. Even though Shinji is the only other person to return, she chooses to be with him in the new Garden of Eden. It is not a fully bloomed feeling hiding in the series, it is a feeling that she begins to express only after she truly sees Shinji for who he truly is.
In the end, Shinji strangles her in the same way he attacked the simulacrum of Asuka who he thought hated him. His form of attacks tells us that he is attacking the image he summoned up to hate him. That image was how he thought others saw him. When she touches his cheek, he relents and releases that it's the real Asuka. I believe that her comment "I feel sick", is either reference to morning sickness or a reference to the difficulties that she and Shinji will face as they face each other and themselves.
Fragments, questions that popped into my head as I watched the movie: There is a great deal of imagery that I have not interpreted or researched. I am specifically interested with 1. The appearance of Rei in the end standing on the lake of LCL. She appeared to Shinji in Tokyo-3 long before. The road means loneliness (as revelaed in episodes 25-26). What does this mean? What is Anno trying to tell us? Is this personal meaning or something that is supposed to have meaning to the audience? 2. Do Asuka wounds at the end correspond to Rei's wounds in Episode 1? What do each of them represent if they do represent anything?