Bah, the Men in Black comics and films are an abomination to the conspiracy theory. Create a Men in Black film with seven foot tall, pale skinned men with telekinetic powers whose goal is to intimidate people who claim to see UFO's. 

More than likely or end up like Rush Hour 3This'll end up the same place as "Ghostbusters III"
A good story line for the third could be striaght from the animated tv show. Remember Alpha? He was a agent who turned bad...superbad. He was insanely powerful and had different organs from different aliens (I think) He was a serious threat and could tone down the zanny elements of the second film.