The return of Annie's Boobs, the monkey, prompted an examination by the study group into their destructive patterns. Chang followed Annie's Boobs into the vents where he discovered the stash of items the monkey had been taking from the group all year.
When Abed revealed Jeff and Britta's secret hookups, the others started chastising them for poisoning the group, only to be reminded in flashback of their own transgressions which affect the stability of the group.
Jeff ended up giving one of his trademark speeches, reminiscent of those he's given before (as shown in additional flashbacks) and the group decided they can get through anything together.
Jeff hurt Dean Pelton's feelings when he made fun of the fact that the Dean frequently barges into their group studies wearing some ridiculous get up. The Dean had an animated dream sequence where he received nuclear waste-induced powers and took the entire study group out.