The second half of the movie is about the waifus that Shinji experiences as a result of the nuclear meltdown, and how he attempts to stop it by using various means, ranging from the most creative to the most idiotic (like getting a feel of the controls), but none of them seem to work.
But it gets better than that: in the final battle, when Shinji is trying to use the final bomb to put an end to the war, he experiences the same waifus that Eva Unit 00 had, and dies fighting.
He dies fighting, and as a result, dies for the sake of humanity.
Thusly confirming that Nagi no asukara is nothing but a fiction created by Shinji and that, as a result, he is nothing but a glorified pawn.
And by the way, that's also why he's barely alive: because the game keeps telling him that he's dying, and he's still in the middle of it.