During the fight against the 13th Angel, Shinji disobeys Gendo's orders and charges into battle to rescue Toji. Gendo does 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. Gendo briefly loses his composure when it happens.
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.
According to the last chapter, he conveniently "forgot" to stop the worm.
The mere fact that Shinji and Asuka not only survived, but thrived and raised a family in the Post-Impact world for so long.