There was the whole "GET THE HELL OUT OF THE OCEAN" thing with the Decepticons.  (There may or may not have been jellyfish involved.)

...And then there's the whole SECTOR SEVEN thing.

...And then there's the whole thing with the Quintessons, making the characters EVIL.

...And then there's Unicron and the Fallen (Tentacles and mayo, anyone? ;D). Other then mind-raping Fireflight and kidnapping a willingly kidnapped Ratbat, that plot hasn't really gone anywhere. There's an unfinished Pokemon battle between Unicron and Primus, though.

...Oh, and some floating skulls that are really creepy and turn mechs into humans or something; no one's quite sure what that's all about. We just flow with it 'cause that's how we roll.

.........And it seems like every week someone gets kidnapped. There may or may not be daring rescues involved with these kidnappings - usually they just turn up by themselves after a few days.

But all in all?  We're usually just drinking/making out/bickering with each other in the common room.  Or painting rotor blades pink.  Or dancing.