Warning Spoilers!
Who is working for who? Seele, Nerv, Gendou???
Fact
Yui, is actually the one who was in charge of this whole thing to begin with. She was the one who
had the original idea for the project which was presented to (at the time) Prof. Fuyutsuki. When
Project E first began the division of Nerv was known as Gehirn. Yui was the one who
introduced Gendou to Seele. Seele was probably the one who was funding the whole project to
begin with. So Seele was above it all. Yui found out Seele's true intentions through the Dead Sea Scrolls,
and told Gendou about it, together they worked to prepare against the final day of Seele's awaited day.
Unfortunately, Yui was lost into Unit-01 which is why Gendou took charge (he was the only one who knew
what was to happen). Gendou must be secretive to hide his plan to counter act Seele, which is why he seems so
mysterious...he seems to work with Seele yet he doesn't mind disappointing them. For example, the Angel that
psycho attacked Asuka, Gendou ordered Rei to use the Lancea Longinus. After the lance was used it was unretrievable,
and this so happens before Seele begins its mass production of the lance. Seele becomes angry that Gendou threw
away the lance, Gendou on the other hand did it on purpose. Why?
Seele obviously doesn't know that he's going to betray them in the end...well Seele gets the idea when
Kaoru, Seele's last messenger is killed and labels Gendou a traitor.
Source: Movie and TV series
UPDATE
The Lance was not solely for protection. It was a tool needed by Seele to conduct the 3rd Impact. It was their way to control Lilith. Gendou got rid of it so he can prepare for his own version of HIP. Gendou also had a plan of his own. Which is evident in ep. 20. But either way, the Lance came back down and well you know the story.
