On the asteroid, Sisko, Kira and Bashir speak to the Maquis and their represenative Cal Hudson. Hudson tries to convince Sisko that out here, on the frontier so close to Cardassian territory, the colonists in the demilitarized zone cannot rely on the Federation to protect them, and this is the only way to defend themselves. Sisko is unmoved, and the group stuns them and leaves.
Sisko returns to Deep Space Nine to find a Federation representative waiting to speak to him and a Cardassian one on the way for the sake. Admiral Necheyev orders Sisko to shut down the Maquis to preserve the treaty, and Sisko agrees, but alone with Kira goes into an impassioned rant demonstrating sympathy for their position. Odo calls Sisko down to security where Quark admits his aid in helping Sakonna secure weapons, and he warns she seemed on a tight schedule — whatever she was planning, it's going to happen soon.
The Cardassian Legate Parn arrives and informs Sisko that Gul Dukat and some accomplices were behind the weapons smugging to the Cardassian colonies in the demilitarized zone. Dukat's allies have been arrested and as far Cardassian Central Command is concerned, Dukat is already dead, likely to be executed by the Maquis. Parn leaves, Sisko not having believed a word he said.
O'Brien tracks the ship that kidnapped Dukat and the Class-M planets it passed, Sisko investigates them with Odo and Bashir and finds the captured Dukat with the Maquis. They rescue Dukat and bring him back to Deep Space Nine, where Sisko informs him of what Parn told him, making it clear that the Central Command has designated Dukat their scapegoat for the Maquis. Dukat offers his aid in shopping the weapon smuggling if Sisko helps stop the Maquis; Sisko agrees. At a staff meeting, Dukat advises that the weapons the Cardassian settlers are getting may be smuggled in using the Xepolites, as Cardassia has done smuggling deals with them before. Sisko, Dukat, Kira and O'Brien find a Xepolite transport, and Dukat talks them into letting them search the ship to confirm they are the weapon smugglers.
The crew learns that there is a hidden weapons depot in a Cardassian civilian center, and the Maquis are planning to attack it within the next fifty-two hours. An attack like this would demand response from Cardassia, and it would quickly spiral into a full war again. Sisko goes to Volan III to try and negotiate with the council and whomever among them may be the Maquis, but the arrival of Hudson makes it clear the entire council is with them. The two again try to sway the other but fail, and Sisko warns that if the Maquis attack the Cardassians, he will be there to stop them.
Sure enough, the Maquis arrive and the crew of DS9 plus Dukat intercept them. One ship is disabled but the one with Hudson aboard is still active. He and Sisko engage in a dogfight, Sisko's runabout loses warp and impulse engines while Hudson loses weapons, so he elects to retreat. Sisko tries to talk him into surrendering, but Hudson will not be moved and leaves, and Sisko stops Dukat from firing at him.
Back on Deep Space Nine, Sisko is congratulated by Starfleet for preventing a war, but he wonders to Kira if he just postponed one.
- Badass Boast: Dukat gets a simple but effective one that cows the Xepolite into surrendering.Xepolite: I don't understand. You're a Cardassian!Dukat: I'm not just any Cardassian. I am Gul Dukat, Commander of the Second Order. You have fifteen seconds to lower your shields or we'll destroy your ship.
- Bittersweet Ending: The Maquis' plans are stopped for now, the Cardassian weapons smuggling into the demilitarized zone is exposed and stopped, and no one on any side lost their lives. But Sisko loses an old friend who sides with the Maquis, it's quite apparent diplomacy is not an option to them, and it's assured the Federation and the Cardassians haven't heard the last of them.
- Combat Pragmatist: To disable a Xepolite ship with its shields up, Dukat advises using phasers to pierce the shields and destroy their bridge, then use the tractor beam to tow the wreckage back to the station. It would work effectively, as well as kill everyone on-board.
- Enhanced Interrogation Techniques: Dukat demonstrates Cardassian preference for these once again. He mocks the Maquis' attempts to mind meld with him, as Cardassian methods to obtain information from captive is more direct and successful. He also offers to "interrogate" Sakonna.
- Good Cop/Bad Cop: Sisko tries to peacefully talk his way aboard the Xepolite ship, and when it doesn't work, Dukat steps in with a more threatening offer they accept.
- Immune to Mind Control: Gul Dukat no sells an attempt by a Vulcan to mind-meld with him to mine information about Cardassian defenses, which he puts down to Cardassian mental discipline.
- Karma Houdini Warranty: Hudson gets away when Sisko can't bring himself to shoot him. But by the time the Dominion wiped out the Maquis, Hudson had been killed.
- The Main Characters Do Everything: The trio of ships sent to stop the Maquis consists entirely of main cast members. Possibly justified given the secretive nature of the mission, but still glaring that an engineer and a doctor are trusted above, say, a few security personnel.
- Mistreatment-Induced Betrayal: Dukat after the Central Command not only abandons him to the Maquis, but also frames him for smuggling weapons into the DMZ. Once Sisko and the crew rescue him, Dukat wastes no time in helping them undo the Central Command's gunrunning plans.
- Poorly Disguised Pilot: Averted. This two-parter establishes the Maquis in order to lay the groundwork for Star Trek: Voyager. However, while it establishes the ideas of the show (showing Klingons, Native Americans, and former Starfleet officers among the Maquis), none of the characters for Voyager appear. In addition, the Maquis would end up playing a much more important story role on DS9 than VOY.
- Proxy War: The Cardassians are revealed to be secretly supplying their colonists with weapons and encouraging them to attack Federation colonies in order to make an end run around the peace treaty with the Federation. When Sisko discovers this he tries to use it to convince Hudson to come back onside and fix the problem through channels, but fails.
- "The Reason You Suck" Speech:
- Dukat gives one to his Maquis captors, telling them that they don't have the stomach to do what must be done.
- Quark gives one to Sakonna, pointing out that with both sides being equally armed it's more advantageous (and logical) in the long run to work towards peace.
- Dukat gives Sisko one for not killing Hudson. Not that Sisko cares.
- Silly Rabbit, Idealism Is for Kids!: Dukat repeatedly mocks Sisko's attempts to use diplomacy and advises that force would be faster and more effective. Hudson gets a jab of the same kind in as well.
- That Man Is Dead: Sisko offers Hudson one last chance to rejoin Starfleet, bringing him his uniform. Hudson chooses to vaporize it with his phaser instead.
- Why Don't You Just Shoot Him?: Dukat chides Sisko and Bashir for not immediately shooting his captors when they storm where he's being held, so he attacks one of them to instigate the shoot-out himself.
- You Would Do the Same for Me: Sisko says this when Dukat thanks him for the rescue. It's unclear to what degree either of them believes that.