What? What's happening to Shinji? Well, it seems that his reality is collapsing. The reality that Shinji made for himself, his perception of the universe and the way he thought the universe perceived him, is coming to an end. The road to complementation will show him how tractable his reality is and lead him towards truth. Understand? Well, watch episode 26 carefully.
But besides Shinji, something similar has happened to Asuka and Misato and perhaps everyone else. Their pasts have resurfaced, their deep-seated fears and troubles dredged up, and their minds cleared.
So, like last week, the question is: what is the Instrumentation of Man Project? Another translation for it is the Mankind Complementation Project. At the beginning of episode 26, we see:
Thus, the answer to this question will be held in tonight's episode. But it will be neither clear to behold nor easy to understand. For his complementation, he will need to reconcile his feelings about his father and understand his own perception and definition of reality.
And what does he gain? Never-ending peace?
[Episode 26 also contains perhaps the best Rei scene in the entire series. Trust me, you will not miss it. -Ed.]