This is really where the psychological part of the Eva series takes off. After going beserk in a test, Unit 03, piloted by Toji Shuzara, the 13th Angel, Bardiel, awakens inside of the Eva. Taking out Asuka and Rei, Shinji comes, but doesn't attack for fear of injuring the pilot. The Dummy Plug system is then activated, and 01 becomes a brutal monster. Toji looses and arm and leg.
After Shinki quits NERV, another angel attacks, taking out Units 00 and 02. Shinji then comes just in time, but Unit 01 runs out of power. After getting its arm cut off, 01 goes beserker, and gets an incredibly high sync ratio of 400 %. Unit 01 begins its "Awakening", eating the 14th Angel alive, and gaining an S^2 engine. Shinji has been absorbed into the Eva.
NERV attempts to rebuild him, while trying to conrol Unit 01, because its binding was melted off when it Awakening happened. While being "rebuilt", Shinji gets trapped inside his mind, going over experiences shut out by him.
This is where the true meaning of the series comes into better view. The mind and heart.