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While Eva 03 is being flown to Japan from the USA, the plane transporting it flies through an odd cloud which is actually another microscopic Angel, which infects Eva 03. During Toji’s first synch test, Eva 03 goes berserk and mutates into an Angel, Bardiel. Possessing both the power of an Angel and the form of an Evangelion, Eva 03 rapidly defeats both Eva 02 and Eva 00. With Toji trapped still alive inside of the Angel, Shinji refuses to use Eva 01 to attack it, forcing Gendo to activate Eva 01’s Dummy Plug autopilot system.
Analysis
Toji points out to Rei that she worries about Shinji; which she herself did not seem consciously aware of before he brings it up. Last episode, he joked about Asuka and Shinji arguing like a married couple. Despite the fact that Toji seems to be the stereotypical "dumb jock", he is actually more perceptive about the relationships between his classmates than they themselves are.
The Angel Bardiel tried to merge with Rei's Unit 00 but not Asuka's Unit 02.
Misato half-jokingly points out to Ritsuko that with four Evangelion units under her command, they could end the world if they wanted to.
Notes
The scaffolding that Eva Unit 03 is carried on as it is flown from the United States to Japan resembles a crucifix.
Eva Unit 03's somersaulting dropkick against Eva Unit 01 mirrors the somersaulting dropkick Eva Unit 01 made against the first Angel it fought, in episode 2.