g-money wrote...
When Shinji Ikari meets up with everyone in the sea of LCL, everyone's saying congratualions - that can either mean they're congratualating him on finding his own identity or he has accepted the Instrumentality Project. However, in End of Evangelion, the Lilith/Rei egg that is taking in all the human souls is broken because Shinji clearly has rejected unison and reclaims his individuality. See the contradiction? It's really open to suggestion at this point.
This is how I see it:
The task of deciding how Instrumentality will play out is given to Shinji. Because he is insecure about having relationships with other people, his choice is to run away to a world in which he is the only person that exists. The entire last episode basically attempts to paint a picture of what is going on inside Shinji's head as he is forced to evaluate his very existence. Throughout his introspection he dwells on how much he hates himself and when he tries to perceive how other people look at him, he finds a reflection of his own inner hatred. In actuality, that isn't the case because during the series everyone is going to great lengths to be there for him and help him, but he only sees that as pity. When he finally comes to see that he does have some value, he is able to realize the appreciation that other people have for him. At that moment, he chooses to reject Instrumentality and return to a world where interaction with other people is a possibility.
The whole scene is just a mental manifestation of Shinji's realization that he does have some purpose and that others do, in fact, appreciate him.