From Star Trek: Theurgy Wiki
The year is 2381. They have been betrayed. Outlawed and alienated by Starfleet Command. Yet in times of war and uncertainty, the persecuted must endure. Ready to answer the urgent call for truth, justice and freedom. They are that crew.
After returning to base in San Francisco after a long diplomatic mission to Romulus, it was due to pure happenstance that the crew of the USS Theurgy managed to pick up transmissions that detailed a horrifying change to Starfleet Command. The senior positions of Starfleet Command - Starfleet's operational authority - included the Commander in Chief, the Chief of Staff and the Chief of Starfleet Operations. These three individuals, along with an unknown number of others in the organization, were revealed through the transmissions to be impersonators of the people they once were; replaced by an unknown enemy.
Before the truth came out, the crew's secretive efforts to meet this threat was compromised, and they had to flee Earth in order to save their own lives. The USS Theurgy was hunted by their former collective fleet - the pursuers merely following orders and whatever fabricated truth Command had given them. The Theurgy escaped after an enduring two months gruesome chase through the Alpha Quadrant. Yet the truth be their witness, they would restore Starfleet to the Federation and the President, and enlighten their fellow brothers and sisters about the immediate danger they unknowingly were in by carrying out the orders of Starfleet Command.
Yet the Theurgy also had to protect the truth they carried at all cost...