When a destabilizing coup takes places on the Tzenkethi homeworld, a newly promoted Captain Sisko is ordered to take the Defiant on a border patrol to evaluate the situation. However, soon after departing DS9 the Defiant develops a series of malfunctions, leading Sisko to consider that they may have a saboteur onboard.

While Jadzia performs the Trill zhian'tara ritual and meets with the previous Dax hosts, Nog undergoes his stress reaction test in preparation for entrance into Starfleet Academy.

When Kai Winn is appointed Bajoran First Minister, Kira becomes concerned about Winn's growing grip on power. However, when the Kai orders Kira to convince her old Resistance leader to return some farming equipment to the government, the situation rapidly descends into a vicious power struggle.

When Quark's mother breaks Ferengi law by wearing clothes and earning profit, Quark and Rom are forced to return home to Ferenginar in order to convince her to confess and make restitution for her crimes. On DS9, Jake eagerly tries to matchmake his father with freighter captain, Kasidy Yates.

An invigorated Sisko returns from Bajor and decides to build a replica of an eight hundred-year-old Bajoran lightship, hoping to use it to prove that ancient Bajoran explorers could have made it to Cardassia before developing warp drive.

When the covertly assembled Romulan-Cardassian attack fleet enters the Gamma Quadrant on a mission of destruction, Garak is forced to interrogate Odo for information on the Founders. Meanwhile, Sisko goes against orders on a mission to rescue Odo.

When a bomb destroys Garak's tailor shop, Odo begins an investigation into who might want the exiled Cardassian killed and why.

Smiley O'Brien from the mirror universe kidnaps Commander Sisko and convines him to impersonate his deceased, mirror universe self in order to persuade the alternate version of his dead wife, Jennifer Sisko, to join the Terran Rebels.

After being assaulted by an alien thief in the infirmary, Dr. Bashir wakes to discover he has a dual mystery on his hands: what happened to the station while he was unconscious and why is he suddenly aging so rapidly?

After receiving a minor dose of radiation poisoning, Chief O'Brien inexplicably begins experiencing a series of jumps into the future. Meanwhile, a Romulan delegation arrives on DS9 expecting an intelligence report on the Dominion in exchange for the continued use of the cloaking device aboard the Defiant.

When Grand Nagus Zek revises The Rules of Acquisition to be more philanthropic, Quark and Rom start to question whether their leader has gone insane. Meanwhile, when Dr. Bashir is nominated for a prestigious Federation medical award, his reaction is less than enthusiastic.

An ancient Bajoran prophecy complicates the first joint Bajoran, Cardassian, and Federation science mission: an attempt to establish a permanent communications link through the wormhole.

Pursuing a Maquis raider to an unstable moon, Kira becomes trapped within an expanding crystal formation that threatens to engulf her. Meanwhile, Nog attempts to persuade a skeptical Commander Sisko to write him a letter of recommendation to join Starfleet Academy.

After a serious accident aboard a Bajoran shuttle, Dr. Bashir struggles to save Vedek Bareil's life while Kai Winn concludes a peace treaty with Cardassia, putting his ethics to the ultimate test. Jake and Nog reluctantly explore the differences between Human and Ferengi cultures.

With history itself at stake, Sisko assumes the role of a pivotal historical figure in order to restore the timeline, even if it means sacrificing his own life.

After a transporter malfunction aboard the Defiant, Sisko, Bashir, and Dax find themselves thrown back three hundred years into Earth's dark past without any means of getting home.

When Ambassador Lwaxana Troi and Keiko O'Brien return to DS9 for the Bajoran Gratitude Festival, residents of the station suddenly become uncontrollably infatuated with one another.

When William Riker from the Enterprise unexpectedly arrives on DS9 on vacation, he takes a liking to Kira, who has also been ordered to take some time off. However, when Kira gives Will a tour of the Defiant, it becomes clear that there's more to Will's vacation than meets the eye.

On an exploration mission to the Gamma Quadrant, the Defiant encounters a unique planet that shifts between corporeal and non-corporeal dimensions. Back on DS9, Quark attempts to create a new holosuite program.

Sisko, Jake, and O'Brien accidentally trigger an old Cardassian security system that believes DS9 has been taken over in a Bajoran workers' revolt and puts the entire station in lockdown.

When a Jem'Hadar infant is found in salvaged spaceship wreckage from the Gamma Quadrant, Odo strives to teach the rapidly maturing soldier to think for himself.

As she travels to Bajor in search of answers about her past, Kira is abducted by Cardassians, surgically altered, and told she is the missing Obsidian Order deep-cover operative, Iliana Ghemor.

When Jadzia begins experiencing violent mood swings and hallucinations, a disturbing secret from Dax's symbiont history reveals a much larger deception.

When Quark lies about killing a Klingon in his bar, he is pulled into a power struggle between rival Klingon families on Qo'noS and forced to marry the dead man's widow. Meanwhile, Chief O'Brien must confront the fact that Keiko gave up her career to join him on DS9.

On his newly discovered homeworld, Odo learns to connect with his fellow Changelings. Back on DS9, Sisko grows concerned that the price the Federation is willing to pay for peace with the Dominion may be too high.

After their violent confrontation with the Jem'Hadar, Sisko takes an untested Starfleet ship, the Defiant, into the Gamma Quadrant in an attempt to make peaceful contact with the Founders of the Dominion.