How many people think that Shinji was right in what he did? (I put a spoiler below if you haven't seen this episode.)
After Eva Unit 01 kills the 13th Angel (Eva Unit 03) and crushes the entry plug that contains the Fourth Child (Toji Suzahara, one of Shinji's best friends), he stays in Unit 01 and threatens to destroy NERV.
His father activated the dummy plug system that automated his Eva and caused the injury of his best friend, and Shinji felt as if it were his hands that did it (the synchronizaton units were still active).
In retribution of his son's "petulant child" actions, he forces Shinji out of the entry plug.
Since then, he sounded much more sure of himself. He finally realized he truly hates his father, and decides to turn his back on NERV. His father accuses him of "running away again" and that they will "most likely never meet again". Shinji tells him "That's fine with me."