Contains spoilers for this episode and earlier episodes.
Shinji refuses to leave Unit-01 after the destruction of Unit-03, demanding that his father answer for the attack on its pilot. Gendo has him rendered unconscious and removed. Toji survives in hospital, where Hikari visits, but Shinji will no longer accept the assignment that injured his friend. He resigns and tells Gendo he does not want to see him again. Misato drives him to the station, explaining that his classmates are potential Eva pilots and admitting the burden she has placed on him. Before Shinji can depart, another emergency begins. A powerful Angel breaks through Tokyo-3's defenses and reaches the Geofront, overwhelming Nerv's preparations.
Asuka's weapons fail against the new enemy, which disables Unit-02 with ease. Unit-01 rejects both Rei and the dummy system, so Rei takes her damaged Eva into battle with an explosive device. That attempt also fails. Watching from below, Shinji meets Kaji at his garden and is urged to choose for himself what he can do. He returns to the cage and demands to pilot. Unit-01 intercepts the Angel inside headquarters and drives it outside, but its battery expires before Shinji can finish the attack. The Eva then reactivates without normal power, violently defeats the enemy and consumes it. Its restraints break apart as Nerv realizes that control has slipped away.