The closing scene of the movie is vague and highly interpretive, where Shinji manages to separate himself from the collective human existence, with Asuka following. Their interaction shows a wide range of positive and negative human emotions. The world remains irreversibly changed, however, and what happens from there is only hinted at. This scene has caused several controversies as to its interpretation.
Some fans have speculated that Asuka may be the amalgamation of Asuka, Rei, and Misato because of her apparent red/brown eyes, the same color as Rei's / Misato's. In addition, she is wearing bandages that correspond to the physical damage she suffered during her last fight in Unit-02 (pierced left eye, injured right arm) which mirror Rei's from the opening of Neon Genesis Evangelion. Furthermore, Rei appeared to Shinji above the ocean of LCL moments earlier.
This theory has been around for a while. One point against the theory is that Asuka's eyes are blue, not brown, at the end of the film, as a scan of the Cardass Wide Card for the scene in question shows. (They look somewhat greyish, but this is because of the color tones/lighting of the scene). [1]
Shinji rejected the Human Instrumentality Project, and as such he has no control over whatever happens next. He is an ordinary boy. Yui says earlier in the film that anyone who can "imagine themselves in their own heart" can come back, on their own. Asuka is one of those people and re-emerged from the LCL pool after her own mental journey (partly shown in episode 25) was complete.
The closing line, "気持ち悪い。" ("Kimochi warui."), spoken by Asuka, likewise can be interpreted in a number of ways. It was translated on the Manga DVD as "How disgusting", but it can also be translated as "I feel unwell", "What a disgusting feeling", "Feels bad", "I feel sick", etc. This has caused much confusion among Western fans, though the true meaning of the line is undefined for the Japanese as well. A recent episode of a Japanese show dedicated to animation described this final line and its original meaning. Initially the final line was written as, "I'll never let you kill me," but Anno was dissatisfied with this. In the episode Asuka's seiyuu, Yuko Miyamura, described what Anno told her he was going for with this scene: Concerning the final line we adopted, I'm not sure whether I should say about it in fact. At last Anno asked me "Miyamura, just imagine you are sleeping in your bed and a stranger sneaks into your room. He can **** you anytime as you are asleep but he doesn't. Instead, he masturbates looking at you, when you wake up and know what he did to you. What do you think you would say?" I had been thinking he was a strange man, but at that moment I felt disgusting. So I told him that I thought "Disgusting". And then he sighed and said, "I thought as much." (1)
However, Tiffany Grant, Asuka's English dub voice actor, says this: The most widely circulated translation of the last line of EoE is "I feel sick", but Amanda Winn Lee (voice of Rei Ayanami, who also directed EoE) said she asked several translators, and she felt "disgusting" was the most accurate adaptation. You could say she is disgusted with/sick of the situation or with Shinji himself. My favorite explanation though, is this one: My husband, Matt Greenfield, directed the TV series and is very familiar with the whole Eva franchise. Matt has said that although (Eva creator) Hideaki Anno seems to change his mind frequently about what various things mean in Eva, Anno once said that Asuka's comment about feeling "sick" was a reference to morning sickness. Now THAT gives ya something to think about, doesn't it! Of course, Anno is quite passionate about the idea that every person should decide for him or herself what Eva means to them.(2)
Another explanation can be found on an Evangelion trading card: the scene "ONE MORE FINAL: I need you." affirms Shinji's choice to return to reality, and in doing so has separated himself from Asuka once more. His first impulse is to strangle her, to finish what he started during Instrumentality, but once he feels her caress (which is very similar to the one he received from his mother only moments before), he realizes what he's doing. He releases his grip and collapses as an emotionally broken little boy, which disgusts Asuka. This presents a more human response in showing Asuka's opinion over Shinji's behavior, but the act of caressing his cheek may represent a better connection between the two, since it deviates from Asuka's normal response to fight back or slap Shinji.
Another interpretation involves what has happened to Asuka during The End of Evangelion: she has just woken from a long coma, only to be torn to shreds inside EVA-02, die (supposedly) and awaken after Instrumentality's failure to being strangled by Shinji seconds before delivering the line, it may in turn just be her reaction to what has transpired.
Despite the somber ending, there are clear references that there is the possibility that every living thing or person who "died" as part of Instrumentality can be returned to their normal state. In fact, both Rei and Yui comfort Shinji and tell him that people can be restored if they want to, depending on the strength within their hearts. This being said, it is obvious that Asuka is the first person to manifest herself back into reality. Another Evangelion trading card explains: "In the sea of LCL, Shinji wished for a world with other people. He desired to meet them again, even if it meant he would be hurt and betrayed. And just as he had hoped / wanted, Asuka was present in the new world. Only Asuka was there beside him. The girl whom he had hurt, and who had been hurt by him. But even so, she was the one he had hoped/wished for...."
Many also speculate that because a lambent image of Rei in a school uniform was either present over the bodies of the already dead during the soul collection (as the case with fallen NERV personnel) or present at their death (such as Misato and Ritsuko), it could be said that their souls were in fact collected either before or after they died and that they can all return one day. However, Yui's quote may only pertain to those who actually died during Third Impact. Thus, it leaves much up to the viewer to decide whether or not the rest of humanity returns. This kind of choice could be analyzed as parallel to Shinji's choice in what kind of world he wanted, and perhaps was intentionally planned out that way, as it leaves the viewer as "God" of the fate of the post-Third Impact world.
