In DS9's Paradise Lost episode (season 04, episode 12), the plot is heavy with Starfleet intrigue: Sisko discovers that Admiral Leyton is plotting to take over control of Earth and put it under a military rule. His options seem limited to convincing the President of the United Federation of Planets of the plot, or convince captains working for Leyton to stop obeying orders.
The fact that these seem to be the only options seems suboptimal. Are there no other high-ranking Starfleet officers (fleet admirals, maybe?) in the chain of command between one of (presumably, many) admirals and the president of the Federation? Is there no official process (involving Internal Affairs, perhaps) to deal with claims of misconduct?