If memory serves correctly (I haven't seen the series in years), Shinji is ultimately fighting his inner self. He cannot comprehend his current situation and denies it (thus denying humanity at the same time). However, over the course of his "trip" he realizes that he is not alone, and that there has always been people there, and many of them friends and family. Realizing this he accepts his fate and thus does not ultimately doom humanity to oblivion. Or something like that. (I may be mixing some things up).