Jeepers, couldn’t President Trump just order them to cooperate?
If he can’t, who’s in charge of the FBI? Are they their own branch of the government?
Yes he could, but it wouldn't make a bit of difference. The DOJ, FBI, CIA, and now the DoD see themselves as independent actors and not subject to what the President directs. The DoD is now the lead actor for removing Trump from office now that the other agencies have failed in stopping him. Esper and his generals/admirals are locked and cocked to make the move.