The Maquis (Star Trek: Deep Space Nine)

As a Cardassian transport, the Bok'nor, prepares for departure from Deep Space Nine, a man in a Starfleet uniform surreptitiously makes adjustments to some nearby equipment. Shortly after departing, the vessel explodes, killing everyone on board.

While the crew begins an investigation, Starfleet sends Lieutenant Commander Calvin Hudson, Federation attaché to the new demilitarized zone along the Cardassian border, to advise and assist. Hudson, an old friend of both Commander Sisko and Dax, confides in Sisko his dissatisfaction with his assignment; he believes Starfleet abandoned the colonists, and that their trust in the Cardassians to honor the treaty is naive.

When Sisko returns to his quarters that evening, he finds Gul Dukat waiting for him. Dukat explains that he is there "unofficially", without the knowledge of Cardassian Central Command, to help Sisko find the truth. On Dukat's request, the two take a runabout to the demilitarized zone, where they detect two Cardassian vessels attacking a Federation merchant ship. The attackers ignore Dukat's orders to stand down, but before the runabout can intervene, an unidentified Federation vessel appears and destroys the Cardassians.

Meanwhile, a Vulcan associate of the saboteur, Sakonna, approaches Quark to negotiate a business arrangement, which he is surprised to learn is an attempt to acquire a wide array of weapons. Elsewhere on the station, the saboteur is abducted by unknown assailants.

Sisko and Dukat arrive at a colony in the demilitarized zone to find Hudson and several colonists in a heated debate with Gul Evek, Hudson's Cardassian counterpart. Evek produces a recorded confession from the Bok'Nor saboteur, identified as William Patrick Samuels, then brings in Samuels' corpse, claiming he committed suicide, sparking outrage from the colonists. Hudson later privately concedes that Samuels may have been guilty of the sabotage, but claims that the colonists have a right to defend themselves, and warns Sisko about the Cardassians again. On the way back to DS9, Dukat vehemently denies Hudson's assertion that the Bok'Nor was transporting weapons.

Chief O'Brien confirms that the device that destroyed the Bok'Nor was of Federation origin. Sisko has Dukat's quarters secured as a precaution, but Sakonna and several colonists manage to kidnap him. A group in the demilitarized zone calling itself "The Maquis" claims responsibility. Sisko, Major Kira, and Dr. Bashir track the kidnappers to a planet in an area known as the Badlands, where they are captured by armed Maquis members, with Hudson revealing himself as their leader.

Sisko demands to see Dukat. Hudson accuses Sisko of siding with the Cardassians over him. Hudson claims the Maquis want only peace, while Sisko characterizes their desire to retaliate simply as revenge. After Sisko declines an offer to join, Hudson and the Maquis stun the group and depart.

Admiral Nechayev is waiting for Sisko when he returns to Deep Space Nine. She refers to the Maquis as "a bunch of irresponsible hotheads" and instructs Sisko to reason with them, seemingly unaware of the true nature of the situation. Legate Parn of the Cardassian Central Command then arrives, and as Sisko prepares to meet him, Odo reports that he has caught "one of the Vulcan's accomplices". Sisko arrives to find Quark in a holding cell.

Quark eventually reveals that he arranged for Sakonna to acquire weapons, unaware of the Maquis at the time, and believes Sakonna is planning an attack within the next few days. Parn then admits that weapons have been smuggled into the demilitarized zone, informing Sisko and Kira that the Cardassian Central Command blames Dukat, claiming he is acting as a renegade, though Sisko and Kira consider it clear they are merely setting him up as a scapegoat.

At a Maquis base, Sakonna attempts to establish a Vulcan mind meld with Dukat, which he easily resists. Sisko, Bashir, and Odo arrive and interrupt the interrogation, and try to resolve the situation peacefully, but Dukat grows impatient, triggering a firefight. The Maquis are captured, but Sisko lets one of their leaders go to deliver a message to Hudson imploring him to settle things peacefully. They bring Dukat back to Deep Space Nine, where they inform him of Parn's accusations. With Dukat's help, they catch a Xepolite trader transporting weapons on behalf of Central Command.

Quark talks Sakonna into revealing to Sisko that the Maquis are planning to blow up a Cardassian weapons depot in the next 52 hours, but she does not know where it is. Dukat promises to find out the depot's location, and in the meantime, Sisko visits Hudson one final time, imploring him to reconsider abandoning his career. Hudson resolutely declines, vaporizing his Starfleet uniform with a phaser.

The DS9 crew is waiting in runabouts when the Maquis arrive at the depot, and as neither Hudson nor Sisko wants to hurt the other, they attempt to disable one another. Finally, only Sisko's runabout and Hudson's raider remain, with Sisko's engines and Hudson's weapons inoperable. Over Dukat's objections, Sisko allows Hudson to escape. Ultimately, Sisko wonders if he has prevented a war or merely delayed the inevitable.