With the conflict between the Klingons and the Cardassians taking its toll, a shipment of desperately needed replicators destined for Cardassia is set to pass through Deep Space Nine. Odo and Lieutenant Commander Eddington of Starfleet Security recommend heightened measures to deter both the Klingons and the terrorist group known as the Maquis, then reveal some troubling news — they believe there is a Maquis smuggler aboard the station, and they have shreds of evidence that the smuggler is Kasidy Yates, Sisko's romantic interest. After hearing the basis for their suspicions, Sisko gives the go-ahead to find a reason to search her ship.

When Kasidy tries to leave for her next delivery, Odo insists on making an emergency health inspection of her ship. Upset that the inspection will make her miss her rendezvous, Kasidy appeals to Sisko, who grants her permission to leave. However, he has the Defiant follow Kasidy and observe her actions. Suspicions are confirmed when her ship meets a Maquis vessel in the Badlands.

Back at the station, Eddington and Worf brief Sisko on their findings. When Kasidy returns, Sisko is clearly uncomfortable. Later, when Odo and Eddington recommend following Kasidy's ship to its next rendezvous and arresting all parties involved, Sisko is forced to agree — and chooses to command the Defiant, leaving behind Eddington to wait for the replicators. Sisko makes a last-ditch effort to stop Kasidy, suggesting she let her first officer handle the delivery instead. Kasidy tells him she has to honor her commitment, then leaves.

On the Defiant, Sisko follows Kasidy's vessel in the Badlands, but no Maquis ship arrives to meet her. After waiting for several hours for a rendezvous to happen, Odo suspects that this may all be a ruse to lure Sisko away from the station. They beam aboard Kasidy's ship and Sisko demands to know why he has been baited, but she reveals that her orders were only to meet a Maquis ship-which has still not arrived. Meanwhile, back at the station, Eddington pulls a phaser on Kira, knocks her unconscious, then takes control of Deep Space Nine.

Realizing the truth, Sisko hurries back to the station, but he's too late. A Vulcan freighter has already taken the replicators, and Eddington, a Maquis spy, has gone with it — leaving Sisko coldly determined to see the traitor court-martialed someday. However, when Kasidy returns to Deep Space Nine to turn herself in for her crimes, Sisko is much warmer. Kasidy admits her love for him, and Sisko promises to wait for her if she goes to prison.