DS9 Season 3 Episode 26 The Adversary

Plot

At a ceremony marking Deep Space Nine's commanding officer Benjamin Sisko's promotion to the rank of captain, visiting Ambassador Krajensky tells Sisko that the Tzenkethi, an alien race with a history of hostility toward the Federation, have unseated their ruler, the Autarch, in a coup d'etat. Warning that the Autarch's replacement might renew anti-Federation hostilities, he says Sisko is ordered to bring the Defiant on a "saber-rattling" mission along the Tzenkethi border.
Along the way, the crew loses control of the ship's critical systems, including navigation and weapons, and Chief O'Brien's investigation reveals sabotage. When O'Brien and Lt. Dax search the crew, Krajensky is revealed to be a Changeling impostor, who flees into the depths of the ship; the crew infer that he has taken control of the ship to cause a war between the Federation and Tzenkethi. Hours of searching cause paranoia among the crew, as the Changeling could be disguised as any of them. Sisko orders Dr. Bashir to administer blood tests to the crew to identify the Changeling, and the tests seem to reveal Lt. Cmdr. Michael Eddington as the impostor; but in fact the Changeling was disguised as Bashir in order to fake Eddington's blood test, and escapes again.
As a last resort to prevent the ship from attacking the Tzenkethi, Sisko readies the ship's self-destruct system, while O'Brien tries to override the Changeling's control of the ship's systems. Constable Odo, a Changeling who has rejected the Dominion, fights the infiltrator in the engine room and kills him, thus becoming the first Changeling to harm another. O'Brien regains control of the ship and Sisko cancels the self-destruct. When they return to Deep Space Nine, they learn that the real Ambassador Krajensky was kidnapped and replaced by the Changeling impostor before ever arriving at the station, and the report of a Tzenkethi coup was false; the entire affair was a Dominion plot to destabilize the Alpha Quadrant. Odo repeats to the others the Changeling's last words: "You are too late. We are everywhere."