The Federation plans to deliver several replicators through Deep Space Nine to Cardassia following attacks by the Klingons that debilitated their industrial base. Lieutenant Commander Michael Eddington debriefs the senior command staff that the Federation and Starfleet fear that the shipment will be intercepted by the Maquis. Eddington and station Security Chief Odo warn Captain Sisko that they believe his girlfriend, freighter captain Kasidy Yates, is working with the Maquis. Sisko denies it but instructs Worf in the Defiant to follow Yates' ship, the Xhosa, when it next departs. Worf confirms that the Xhosa delivered supplies to a Maquis ship in the Badlands.

Disheartened, Sisko insists to be present when they attempt to catch Yates' next shipment once they hear of its schedule. He, Odo, and Worf wait aboard the Defiant at the expected time but the Xhosa does not show up. Odo suggests this might have been a ruse to lure Sisko away from Deep Space Nine. However, the Xhosa soon does arrive, and Sisko tasks Yates to her actions. Yates claims she has only been delivering medical supplies to the Maquis, but for herself, she suspects that maybe she too had been used by the Maquis to lure her from the station. Fearing deception, Sisko lets Yates go and sets course back to Deep Space Nine.

Meanwhile, with Sisko's absence, Eddington takes command and orders the senior crew to prepare transport of the replicators to an inbound Vulcan craft. Major Kira walks into the storage bay where Eddington is alone with the replicators, and he knocks her unconscious, revealing himself to be with the Maquis. Eddington transports himself and the replicators to a waiting ship and flees the station. Eddington later contacts Sisko to reveal his alliances and that the Maquis are only at conflict with Cardassian, though promise further trouble if the Federation aids them. Sisko vows to capture and arrest Eddington himself. Later, Yates returns to the station alone, having dropped her crew in the Maquis Badlands as to turn herself in, believing this was what Sisko wanted. She tells Sisko that she had intended no harm and only felt a duty to aid the Maquis. Sisko and Yates have an emotional embrace before she is taken off to the brig.

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