[Renegade334]

Originally Posted by D a m i e n

Spoiler:

for some reason i always thought that it was gendo's plan to have the boundary between humans and communication problem solved he used the funds from the SEELE and worked on his own agenda while the SEELE wanted to something that is way too blurry in my memories ( maybe world domination or something like that) and that s was why the SEELE attacked the NERV.

Spoiler:

The reason why SEELE stopped backing Gendo and ordered to wipe out the entire Geofront was because too many things were getting out of hand...and strayed from their precious scenario. Unit 01 acquiring an S2 engine of its own was one of those infuriating developments (as there can be only one God in this universe, not two)...and in the manga they were also clearly annoyed Shinji had been made the 'son of an artificial god' (in reference to his 'rebirth' from Unit 01 after he got absorbed).

Also, they had come to the (correct) conclusion that Gendo was trying to gain control on Third Impact and from there on they needed to intervene before they could lose their weight upon Mankind's pre-programmed destiny. They had a dream of raising Humankind into a single, godlike entity and Gendo, with his wish to be reunited with his 'departed' wife, was seriously endangering the said project. And they obviously couldn't allow that.