Ik this is too late, basically he reject his humanity to be immortal, have Tabris level of power so he can complete his Human Instrumentality alone and see Yui again.
okay so in more details Gendou, during 3.33, obtains the power of Adam. In doing so, he rejects his humanity to start the fourth impact to be with Yui in 3.0+1.0. By doing this, he needs both spears of Longunis and Cassius and Eva-Unit 13 to be awakened which we saw in 3.33 with Kaworu being the 1st angel but being demoted to the 13th (last angel) so with Asuka awakening of 3.0+1.0 after using the angel powers Eva-13 consume Asuka which then Awaken the unit. Later Gendou fights with Shinji and in doing so Longunis and Cassius extinguish the powers/life of the spears to be sacrificed into Black Lilith (all part of his plan), which would then come out of Eva's imaginary, which is connected to Golgotha Object, which is seen as a device that holds countless universes and timelines of Evangelion, past, present, and future. Black Lilith came out and then was "killed" by the Spear of Gaius which was handed to Shinji and then to Gendou after he was reunited with Yui which at the end Gendou and Yui sacrificed themself along with all the Evangelions. Humanity survive and came along Shinji wish to keep everything the same except a world without Eva's and Angels. The End.
