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During the fight against the 13th Angel, Shinji disobeys Gendo's orders and charges into battle to rescue Toji. Gendo responds like he originally did and has the Dummy Plug activated... for a few seconds before EVA-01 rejects it, allowing Shinji to carry on as he expected. This shocks Gendo so much he briefly loses his composure.
Shinji: Thank you, mother!
During the Battle of Tokyo-3, Toji arrives to fight the JSSDF and the MP-Evas... Piloting the Jet Alone!!
Kaji blackmails the Prime Minister with a computer worm that'll release all the facts about SEELE and Second Impact.