Earth has been placed under martial law due to a seemingly imminent Dominion invasion, but Benjamin Sisko believes that there is more going on than meets the eye. With the aid of Cadet Nog and Odo, Sisko gathers evidence Leyton is planning a coup and goes to Federation President Jaresh-Inyo. Politics and lack of definitive evidence tie his hands.
Around this time Sisko is confronted by a shapechanger in the guise of Chief O'Brien. He tells Sisko there are a few other Changelings on Earth and then escapes.
Admiral Leyton, the suspected ringleader of the conspiracy, has Sisko framed as being a Changeling. Odo breaks him out of prison. Contact with the Defiant is made, as it is learned that Leyton's reach even extends to the station. A Starfleet officer there had affected the wormhole, starting the entire crisis.
Unfortunately, Leyton has convinced the USS Lakota that the Defiant is crewed by changelings and the two ships are forced into battle. Sisko confronts Leyton at phaser point. The plan falls apart when the DS9 conspirator talks and the captain of the Lakota refuses orders to kill the Defiant crew. Leyton resigns.