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 undermine Sisko's efforts.
Around this time Sisko is confronted by a Changeling in the guise of Chief O'Brien. He tells Sisko there are actually only a total of four Changelings on Earth, and mockingly points out to Sisko how much panic they have caused, drastically out of proportion to their actual numbers. The Changeling then walks away.
Admiral Leyton, the suspected ringleader of the conspiracy, has Sisko framed as being a Changeling. Odo breaks Sisko out of prison. Contact with the Defiant is made, and it is learned that Leyton's reach even extends to the station: a Starfleet officer on DS9 had affected the wormhole, creating the impression of a cloaked Dominion fleet entering the Alpha Quadrant and 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 conspiracy falls apart when the DS9 conspirator confesses and the captain of the Lakota refuses orders to destroy the Defiant to prevent evidence against the conspiracy from reaching Earth. Leyton resigns.