Fuyutsuki, Kouzou

Given later revelations about apparent decades-long behind-the-scenes machinations of SEELE into all aspects of the sciences directly and indirectly involved in the subject of Instrumentality (the Dead Sea Scrolls were uncovered in 1947, so presumably the world-wide conspiracy behind SEELE's operations had been in existence for only slightly less time) it is safe to say that Professor Fuyutsuki had been monitored by and targeted for recruitment by SEELE early in his career. If speculations regarding Yui actually having been a junior member of SEELE through her father's influence are correct, then Fuyutsuki's association with Gendo Rokoboungi/Ikari was equally planned well in advance. His earlier introduction to Rokoboungi/Ikari by taking him on as a research assistant, bailing him out of jail, and later meeting him again after Second Impact during a research expedition to the area formerly occupied by Antarctica may be seen as steps in a testing procedure to determine his reliability, discretion and intelligence at being able to surmise SEELE's goals...and whether he would actually be amenable to that recruitment.

Fuyutsuki's earlier assessment of Gendo Ikari's personality (in the Director's Cut, the subtitle during Fuyutsuki's recall of the initial meeting at the police station refers to Rokoboungi/Ikari as 'real bastard') was reinforced by the Antarctic mission, during which Fuyutsuki began to suspect that the now Gendo Ikari's associates in SEELE may be more powerful and dangerous than he originally realized. The seed of doubt planted during that voyage led to the discovery of the true nature of the events leading up to Second Impact and SEELE's involvement in initiating that catastrophe.

After Fuyutsuki threatened to expose Gendo to the public, regarding the massive deception concerning Second Impact, in 2003 (through his own research), Gendo Ikari led him into the GeoFront and Central Dogma and revealed to him an incomplete prototype Eva. At that point, Ikari asked Fuyutsuki to join him and "create a new future for humankind, together with me." Fuyutsuki accepted this, and started to help Gendo. Whether this agreement was entirely out of idealism or more from self-preservation is not made clear. In the movie The End of Evangelion it is mentioned that SEELE had threatened Fuyutsuki with being 'disappeared'; the implication is that this recruitment may have been a Hobson's Choice.

Despite Fuyutsuki's initial dislike of Gendo, it is clearly evident that he becomes the closest thing that Gendo has to a confidant in the series. In many episodes, Fuyutsuki may be seen as a sort of external conscience for Gendo Ikari; despite his somewhat gruff nature, Fuyutsuki is genuinely concerned for those under his commend, but having the added knowledge of SEELE's true goals for Instrumentality, must balance his compassion with Ikari's ruthlessness in pursuing both SEELE's agenda and Ikari's own hidden one of re-uniting with his discarnate Yui. Ikari's dependence upon Fuyutsuki as both confidant and his chief lieutenant is shown by the many times that Fuyutski takes the initiative for action without waiting for direction from Ikari.

As had been mentioned and implied in the series, while obviously kindly disposed towards Yui, at all times Fuyutsuki maintained a professional demeanor towards her. It is not intimated how the Destrudo experiment that 'killed' her and ensconced her soul into EVA Unit 01 affected him. The depth of his feelings for her, however, is revealed when immediately prior to dematerializing into LCL during Instrumentality, Fuyutsuki witnesses an image of Lilith-as-Yui which appears to float down to embrace him, comforting him in his transition to a non-corporeal state.

(Source: afufu.net/freewill/)