All because NERV got a hold of SEELE's full laundry list of misdeeds and the radical faction within SEELE went nuke-happy behind Keel's back to cover it up, kickstarting a chain of events that ultimately ends in 99% of humanity being perma-killed beyond resurrection via Instrumentality. On the other hand, when the reformist Angels try exploiting the situation to offer NERV a deal to team up against the loyalist Angels, Kaworu, friendly and benevolent Kaworu... loses it a tiny bit. Not much, just enough to smack the the Archangel who came to deliver the deal in the face.
With the Moon.
But hey, NERV now has a spiffy, although slightly decayed, space fortress that can house over a million people, craps out multiple Wunders and Evas per year and has enough dakka to potentially take on the entire rest of humanity's collective military power and stand a fair chance at winning. Mind you, they don't actually try that last part because they understandably don't have the manpower to fight a full-scale war even with exclusive access to Evas. Especially since despite being nigh-unstoppable engines of destruction on the ground, Evas are flying bricks in zero-g against anything smaller than an Angel due to their mass and bulk.