“There are also those who desired this disastrous outcome. A world untainted by original sin that no man may enter.”
Gendo abandoned his son, Shinji, when he was a toddler and throughout the series he was uninterested, distant, and harsh towards Shinji. In the movie, The End of Evangelion, Gendo and Rei are in Central Dogma in front of Lilith. He asks Rei to lower the A.T. Field so he can see Yui, his deceased wife again. Rei is supposedly made from some parts of Yui and when her AT field is lowered she and Gendo will dissolve into the “soup of life” (or “primordial goo”) uniting Gendo with the pieces of Yui. She denies him saying, “I will not be your puppet” and cuts off part of his hand into her body. Despite his want to be reunited with his wife he has affairs with Naoko Akagi, the developer of the Magi, and her daughter Ritsuko Akagi, head scientist of NERV. There is no love in these relationships and only does it to gain their favor or have them keep secrets.
In NERV, Gendo is responsible for the research done on the Evas and theHuman Instrumentality Project. He is the father of the Third Child, Shinji Ikari. At the start of the series, he is the only person having an effective connection to Rei Ayanami.
Gendo is a brilliant scientist and politician (the master of puppets in the series) who works diligently for his organization; however, he is an extremely cold and distant father towards his son, and has no qualms about using and discarding people to achieve his goals:
“Gendo is the type of person who can see & think about the welfare of an organization as a whole. In other words, he’d do anything to succeed. He takes drastic and extreme measures, by fair means or foul, or by hook or by crook, in order to accomplish his own purpose. In some ways he’s mean, he hardly cares about Shinji.”
His last lines in The End of Evangelion reveal his regret and the true motivations for his ruthless behavior. He intended to use Third Impact to bring his wife Yui Ikari back to life. However, he realizes that his efforts are in vain and that he ignored the real wishes of Yui. She intended to bring about a brighter future for their son Shinji, whom Gendo has sacrificed in order to bring her back. In essence, Yui’s dreams and principles were violated to resurrect her. Shortly after,Unit-01 is shown grasping Gendo in its hand before decapitating him, clearly rejecting Gendo’s actions (however, this death sequence is questionable, due to its surreal appearance).