Shinji was depressed and wanted to commit suicide.
Rei was also down, and wanted to return to Lilith.
Asuka was also down, and was busy being a puppet.
In the meantime SEELE is initiating their plan for world domination through unifying all souls onto one, with themselves at the top. They were going to take out Gendo and NERV first to get hold of their trump cards, which are Lilith, EVA01 and other various secrets.
But when EVA01 comes out of the ground to greet them, they seize the opportunity to start third impact right then and there, using Shinji's depression as a catalyst. His will to end himself, the destruction of his ego will fulfill everything.
But at the same time, Rei decides to deny Gendo his victory, and talks some sense into Shinji. This then allows Shinji and everyone else to come back eventually.