Kasidy Yates wakes up in Captain Sisko's bed, kisses him on the forehead and gets up to leave. Sisko reaches out and pulls her back into bed telling her that a meeting with her engineer can wait. Kasidy finally leaves after joking about his style of command and tells him that she will see him later. He pulls her now vacant pillow over, admires her lingering scent, and switches it with his own.
In the wardroom Commander Eddington is giving Sisko, Major Kira, Commander Worf, Commander Jadzia Dax and Odo a briefing on very sensitive information from Starfleet Command. The Cardassian civilian government has secretly contacted the Federation Council with a request for industrial replicators to help build new power plants and factories. The Federation has agreed to provide twelve class-four replicators; however, the information must be kept secret because Starfleet Intelligence believes the Maquis may attempt to seize the replicators for themselves. Since the Klingon invasion the Cardassian military has been unable to pay much attention to the Maquis, so Sisko orders the crew to take the necessary precautions in anticipation of the shipment's arrival as it passes through Deep Space 9.
As the other officers leave the briefing Odo and Eddington stay behind to talk to Sisko. They tell him that they have reason to believe there is a Maquis smuggler on the station, and that they think it might be Kasidy Yates.
Sisko is upset to hear the security officer's suspicions and demands evidence. They tell him that Yates has been suspiciously late in her normal cargo runs and that Starfleet Intelligence believes a Maquis contact had begun living on the station about the same time that she did. Sisko believes the evidence is very slim, but tells them to look for a way to discreetly search her ship.
Doctor Bashir and Garak are sitting in a crowd of spectators watching a springball game when Bashir notices that Garak seems to be more interested in watching Ziyal (who is also in the crowd and trading glances with him) than the game, which is being won by Kira. He warns Garak that he should leave Ziyal alone considering how much Gul Dukat hates him, but Garak doesn't seem interested in the Doctor's advice,
In his quarters, Sisko is cooking a meal when the door chimes. Kasidy Yates enters, followed soon after by Jake, who asks if either of them know what a Kavarian tiger-bat smells like. He's writing a story and wants to make it as realistic as possible. Captain Sisko uses the situation to ask Kasidy about her cargo route, which is in the general vicinity of Kavaria, but drops the subject when she becomes curious about his interests in her flight plans.
Ziyal and Garak find themselves alone in a turbolift. Garak breaks their awkward silence with a joke and after a brief exchange, they part on amicable terms.
Odo and a pair of his deputies are talking to a Bolian crewmember of Kasidy's ship as she walks up. Odo informs her that they need to conduct a class 2 inspection of her cargo before she can leave the station due to a reported outbreak of Temecklian virus on Bajor. Kasidy contacts Sisko and tells him that if they wait the six hours needed for the inspection they will miss their rendezvous with a Tholian freighter. She promises to flood her whole cargo hold with baryon radiation as a precaution, but insists that she needs to leave immediately. Sisko agrees to let her go, but afterwards assigns Worf to take the Defiant and follow her under cloak.
Aboard the Defiant, Chief O'Brien informs Worf that Yates' ship, the Xhosa, has changed course and is heading towards the Badlands; Worf tells him to stay with it. Sensors soon detect the impulse signature of a Maquis raider, and the Xhosa beams over its cargo.
Garak is working in his shop as Ziyal enters. She compliments him on his shop and eventually invites him to try a new holosuite program of a Cardassian sauna that she received from Quark. He accepts and they settle on a time.
Jake enters a room in their quarters to find his father sitting at the table. He gets breakfast from the replicator and sits down, explaining that he's having a dish recommended to him by Kasidy. Captain Sisko says he didn't get much sleep the night before and that he's in a bad mood because he has a lot on his mind.
In the wardroom, Eddington goes over their surveillance of the Xhosa. They have determined that the cargo was mostly organic, probably food or medical supplies, and Dax points out that at least its not weapons. Worf tells Sisko the Xhosa will return soon and Sisko dismisses the briefing.
Sisko is back in his quarters when Kasidy comes in smiling, and he tries to put on a good face, not letting on about what he knows. He tries again to casually ask her about her route, but is interrupted when Jake comes in and invites them to go watch a baseball game holosuite program that Nog has sent him. Sisko declines, saying he has to get back to Ops, and Kasidy protests telling him she has to leave in a few hours for another run. He goes anyway and meets with Odo and Eddington in his office to tell them that Kasidy will be leaving to make another run later that night. They agree to have the Defiant follow the Xhosa again to arrest them and the Maquis if they make another rendezvous. In addition, Eddington tells Sisko that he would rather not be aboard the Defiant for this mission and would instead like to stay aboard the station to oversee security for the shipment of replicators the next day. Sisko agrees and takes command of the Defiant himself.
Sisko catches Kasidy at the airlock of her ship and invites her to leave with him for a spontaneous vacation to Risa, not even stopping to pack a bag. She says the offer is tempting but that she can't go with him and boards her ship to leave.
On board the Defiant, the crew has followed the Xhosa to the same coordinates as their last meeting with the Maquis, but this time there is no Maquis ship to meet them. Sisko decides to sit and wait.
Quark is in Garak's shop getting fitted for a new suit when Kira comes in and pins Garak against a wall, telling him that if he hurts Ziyal in any way she will make him regret it. Kira leaves, and Quark asks if he is still going to meet Ziyal in the holosuite, and Garak says he had been afraid that Ziyal was just trying to lure him there to kill him, but that now he is sure he will be safe because the Major certainly wouldn't have told him not to go if it was dangerous for him to do so. Quark points out that it might all have been part of the plan to get him there, and Garak is left unsure once again.
Back aboard the Defiant, the crew is becoming suspicious of having to wait so long. Odo suggests that maybe they have been lured into the Badlands to get the Defiant away from the station. They decide to de-cloak and beam over to the Xhosa and find out what's going on. Kasidy only knows that she was supposed to meet a ship and knows nothing about what might be happening at the station. Sisko realizes that they must have drawn him away to get at the replicators.
In the wardroom on the station, Eddington is briefing a group of Starfleet security officers about loading the replicators onto a Vulcan freighter. He tells them they are not to discuss it even with the Bajoran security detachment, and the station is to observe communication silence. As he dismisses the security officers, Kira enters the room and asks why Eddington wanted to see her. Eddington takes out his phaser, tells her he needs to take command of the station for a few hours and shoots her. He walks out of the room and locks the door.
The Defiant streaks back to the station, leaving Yates and the Xhosa behind as Odo points out that they'll probably never see them again. Meanwhile, back on Deep Space 9, Eddington leaves the station under the command of Lieutenant Reese and departs aboard the Vulcan freighter.
When the crew arrives back in Ops, O'Brien reports that several starships are looking for the freighter, but Odo is convinced they will not find it, seeing as how Eddington seemed to have prepared for every contingency. They receive an incoming message from Eddington and Sisko takes it in his office. Eddington tells Sisko to leave him and the Maquis alone, saying that if they do, they'll never hear from them again. Sisko tells him that he will find him no matter how long it takes and see to it that he ends up in a penal colony, regretting what he's done.
Garak enters the holosuite to find Ziyal lying on a slab of rock under a heat lamp. He approaches cautiously, and asks why she really asked him to come. She tells him that they are both outcasts and that she had hoped they could find a bond in their mutual exile, despite his history with her family. With her motive cleared up, Garak says he won't be needing the phaser he's brought along and sets it aside to lay on the rock and enjoy the heat with her.
With Eddington's betrayal looming in his recent past, Sisko must now deal with Yates, who has returned to the station aboard the Xhosa. She exits the airlock alone and tells him she did not see the point in bringing her crew back just to face a prison sentence. Sisko tells her that he still has to uphold his duty, and she tells him she understands but didn't want to throw away their relationship even if it meant turning herself in. They embrace and Sisko calls for security to take her away.