When Commander William Riker from the U.S.S. Enterprise visits the station, an intrigued Kira takes him on a tour, particularly of the Defiant. On the bridge of the docked ship, Kira uses her access code in order to show him more of the Deflant's operations. But as the ship springs to life, Riker suddenly stuns Kira with a phaser blast, then a man and a woman, Tamal and Kalita, transport aboard. Riker fakes an emergency on the warship and convinces Sisko to have it freed from the dock. The Defiant then engages warp drive and leaves the sector, at which point it is revealed that the man stealing the vessel is actually Thomas Riker, Will Riker's duplicate, created as the result of a freak transporter accident nine years ago.

Sisko and Odo inform Gul Dukat that Thomas Riker — who is believed to be a member of the Maquis, a terrorist group fighting against Cardassia — has stolen the Defiant. They fear that Dukat's superiors at Cardassian Central Command will assume Starfleet wanted the Maquis to have the warship. This would give the Cardassians an excuse to launch a full-scale invasion into the Demilitarized zone between their territory and Federation space in order to find the Defiant. Seeing no other option, Sisko agrees to join forces with Dukat to help destroy the vessel. Meanwhile, Riker makes a rendezvous with a group of Maquis ships, then gives the order to head for the Cardassian border.

Sisko accompanies Gul Dukat to the Cardassian homeworld's War Room, where they meet Korinas, an observer from the Obsidian Order. Sisko reveals that the Defiant has a cloaking device, but admits the ship may be detectable with an anti-proton beam. Meanwhile, Riker uses a decoy vessel to lure away Cardassian warships, then slips into their territory. Kira then sets off an explosion on board, which disables the cloaking device and causes the Defiant to lose power.

The Defiant is repaired, and Riker reveals to Kira that he believes renegade Cardassians have a secret base in the Orias system where they are building an invasion force. His mission is to destroy that operation. In the War Room, Sisko realizes that the Orias system is the Deflant's destination and suggests that a warship be sent there, but Korinas objects, informing them that the sector is controlled by the Obsidian Order — and any warship that enters will be destroyed.

The Defiant is located heading toward the Orias System and Dukat sends ten ships in pursuit. But he and Sisko are surprised when three more Cardassian warships suddenly appear in the sector, and they realize that the vessels belong to the Obsidian Order. On the Defiant, Riker engages in battle and finds himself at a considerable disadvantage. Then Sisko comes up with a plan. Since Dukat wants to know what the Obsidian Order is hiding, Sisko proposes that he allow the Defiant to safely return to Federation space in exchange for the information on the Orias system gathered in the Defiant's sensor logs after entering the area. Dukat accepts, provided the Cardassians also get Riker as a prisoner. Riker agrees and surrenders to Dukat's forces in order to save his friends on the Defiant, then prepares to spend the rest of his life in a Cardassian labor camp.