Sure, he was just as responsible for the Third Impact as Gendo was, but fans couldn't help but feel invested in his character after learning about his past.
So it's naturally a shocker to find out that not only did Fuyutsuki join Gendo — a man he considered disgusting and troublesome — but he also worked tirelessly to bring about the end of the world with the Third Impact.
Read on to find out!
Why Did Fuyutsuki Join Gendo?
Gendo threatened Fuyutsuki into joining him. When Fuyutsuki first revealed to Gendo that he knew the truth about Second Impact, Gendo explained Project E to him and gave him two choices: he could either join Gendo or be killed for "knowing too much."
Fuyutsuki later confided in Yui about Gendo's threats but told her that it was ultimately a good thing since he could sabotage NERV's plans far better from within than he could do as an outsider. This was likely when Yui proposed her plan to him, and the two set to work.
Once Yui got herself absorbed into Eva Unit-01, Fuyutsuki worked with Gendo on the Human Instrumentality Project.
He would diligently work on the project and continue to act like he wasn't in favor of what was going on — when, in fact, it was his goal to put the Third Impact in place.
His work eventually gained him Gendo's trust, and soon enough, Fuyutsuki was made Gendo's right-hand man and was put in charge of NERVE's operations when Gendo wasn't around.
Fuyutsuki, too, seemed to have grown accustomed to Gendo's tempers. He would go out of his way to ensure that Gendo wouldn't throw another tantrum and knew how to talk to Gendo with extreme patience.
Of course, their relationship was strictly professional, and both men didn't seem to harbor any friendliness or affection towards each other. Still, Gendo couldn't help but feel admiration at respect for Fuyutsuki's genius — something that Fuyutsuki used to his advantage.
Was Fuyutsuki In Love With Yui?
Though it was never explicitly stated, it was made evident that Fuyutsuki was in love with Yui. He'd been attracted to her since the very first time he'd met her, and he seemed visibly stricken when Yui announced that she was going to marry Gendo.
It was obvious in the way he stole glances at her and how he trusted her enough to confide in her about Gendo, despite the two being married.
He never acted on his feelings, though. Maybe it was because Yui considered him her sensei, or he planned to tell her but realized it was too late after Yui told him about her marriage.
Whatever the case, he kept his feelings to himself, even though he never stopped loving her.
Whether or not Gendo knew about this is unclear, but throughout their partnership, there seemed to be a silent understanding that bound them together: they were both doing what they did out of affection for Yui, and they didn't regret it one bit.
What Was Fuyutsuki's Purpose? Why Did He Want To Cause The Third Impact?
Fuyutsuki's purpose was to carry out Yui's plans. He was the only person who knew what Yui intended with the Third Impact and agreed to work with Gendo on the Intrusmentality project in order to ensure that the Third Impact would pan out the way Yui wanted it to.
"I support your intentions - Not Seele's."
— Fuyutsuki to Yui.
He made it clear that he opposed Seele's ideology and that he only trusted and had faith in Yui's plan.
Unlike Seele, both Fuyutsuki and Yui believed in the idea of humanity surviving and hated the thought of humans being erased from existence. Even if he didn't have feelings for her, we're inclined to believe that Fuyutsuki would've agreed to Yui's plans since it gave humans a chance to survive.
"I prefer a world where people live, no matter how stained it is with sin."
— Fuyutsuki to Gendo.
After Yui's death, Fuyutsuki was further motivated to complete the project. Because at the end of the day, he dreamt of reuniting with Yui's soul after the Third Impact — much like Gendo was.