Dr. Nick: There seem to be strings of Angel goo connecting to Toji's body. This, and the timing of the takeover strongly imply that Bardiel needed a pilot inside in order to be able to puppet the Evangelion through them instead of merely using the pilot as a human shield. You could say poor Toji (and Shinji too!) got to experience as a pilot what it feels like to be the normally helpless person inside the core.
(For those of you who are curious, in SRW games you can usually save Toji and Unit-03 by fulfilling secret conditions, although the Eva is a bit underwhelming in actual gameplay because it doesn't really have any distinguishing weapons or gimmicks beyond the pylon-installed spike launcher in its original Alpha appearance. Unit-04 has never been playable, so Kensuke doesn't get a break even in the most self-indulgent of creator-approved fan-fictions.)
