Thinking about this again, one of the key points made is that the dean had to have coordinated all of it, but he's too dumb to have coordinated any of it.

I think Annie must have found out about Jeff's fake class and tattled to the dean. Then they set up the original plan with Garrity and the fake night school stuff.

Since the dean loves Jeff, he couldn't help but tell Jeff what they were doing. I think that probably happened shortly after we met Professor Professorson, so they all knew about the fake car bomb.

Then Jeff told Annie that the dean had betrayed her and for most of the episode everyone knows what's going on, but the dean doesn't know that Annie and Jeff are conspiring against him. The car bomb scene only makes sense if Annie doesn't know that Jeff knows, so he must have started conspiring with Annie after the night school stuff.

The penultimate twist is Annie shooting Jeff because the dean didn't know that Annie and Jeff were conspiring, so that actually surprised him.

I'm sure my theory's full of holes. I better go back and rewatch the entire show.

p.s. The final twist is capped off with one of my favorite lines ever "Fact: In 100% of fake gun related shootings the victim is always the one with the fake gun."