When Odo is plagued by an unknown illness that renders him barely able to hold his shape, Dr. Bashir and Odo see not other option but to track down the Founders. Meanwhile, tensions between the Federation and the Klingon Empire continue to rise.

After learning that he is dying from a rare Ferengi disease, Quark decides to auction his vacuum-desiccated body on the Ferengi Futures Exchange. When an injured Keiko O'Brien returns from an expedition to the Gamma Quadrant, Dr. Bashir must take extreme measures to save the life of her unborn child.

Dr. Bashir attempts to rid a planet of a bio-engineered plague that was sent by the Dominion as punishment for resistance.

After a rogue band of Jem'Hadar attack DS9, the crew of the Defiant reluctantly join forces with a group of loyal Jem'Hadar in order to prevent the rogues from obtaining a dangerous piece of ancient technology.

Sisko is forced to confront the betrayal of someone he cares about when they are accused of being a Maquis smuggler. As the only two Cardassian residents on DS9, Garak and Ziyal begin spending time together.

A mysterious woman arrives on DS9 and encourages Jake to begin writing a novel. Lwaxana Troi, pregnant with a son, unexpectedly visits Odo and asks him to help her escape her husband.

When the counterpart of the long-deceased Jennifer Sisko lures Jake to the mirror universe, Sisko is forced into helping the Terran Rebellian against the Klingon-Cardassian Alliance.

After being convicted of espionage, Chief O'Brien struggles to re-integrate back into his life on DS9 after serving 20 years in an Argrathi virtual prison.

When Worf is accused of destroying a civilian transport ship during an engagement with the Klingons, a hearing is held on DS9 to determine if Worf should be extradited to Qo'noS on charges of murder.

Sisko's role as Emissary is challenged when a 300-year-old Bajoran lightship emerges from the wormhole and the passenger claims that he is the Emissary of the Prophets. Meanwhile, Keiko O'Brien returns to DS9 with some surprising news.

Tired of unfair pay and working conditions, Rom organizes a union for the employees of Quark's Bar and encourages them to go on strike. Meanwhile, Worf has troubling settling into life onboard DS9.

In an attempt to regain his lost honor, Worf's brother Kurn arrives on the station with a troubling request. Meanwhile, Major Kira and Chief O'Brien investigate Klingon activity near the Bajoran border.

Stripped of his former rank, Dukat returns to escort Major Kira to an intelligence sharing conference between Cardassia and Bajor. However, when a Klingon Bird-of-Prey attacks the conference, Kira and Dukat unite to hunt down those responsible.

Odo is forced to confront his feelings for Kira when Bajoran First Minister Shakaar visits DS9.

When Starfleet tightens security measures on Earth and institutes martial law to combat the Changeling threat, Sisko and Odo begin to investigate a suspicious trail of events that imply all may not be what it seems.

After the bombing of a Federation conference is revealed to be the work of the Dominion, Sisko and Odo travel to Earth in hopes of uncovering the Changeling responsible.

A transporter emergency aboard the USS Orinoco replaces the characters in Dr. Bashir's secret agent holosuite program with the physical forms DS9's senior staff.

Klingon Dahar Master Kor, Jadzia Dax, and Worf search a remote planet in the Gamma Quadrant for the fabled Sword of Kahless; the mythical, millennia-old weapon of the Klingon Empire's first leader.

On a shakedown cruise to Earth to drop off Nog at Starfleet Academy, a malfunction on Quark's new ship causes Quark, Rom, and Nog to crash in the year 1947 in Roswell, New Mexico.

When Sisko defends a Karemma ship that has been trading with the Federation without the Dominion's knowledge, a badly damaged Defiant is forced into a dangerous game of cat-and-mouse with two Jem'Hadar ships inside a gas giant.

When Jadzia Dax is reunited with the Kahn symbiont, the wife of one of her previous hosts, together the pair must decide whether or not to defy Trill social taboo and rekindle their former relationship.

Major Kira and Gul Dukat form an uneasy alliance as they search for a missing Cardassian prison ship, the Ravinok, that disappeared six years earlier while carrying Bajoran prisoners. Back on DS9, Sisko is overwhelmed by the prospect of Kasidy Yates living aboard the station when she decides to take work closer to Bajor.

After crash landing on a planet, Dr. Bashir tries to help members of a rogue Jem'Hadar unit free themselves of their addiction to the drug the Founders use to control them. Meanwhile, Worf tries to adjust to life aboard DS9.

When an aspiring writer turns up in the middle of the night, an elderly Jake Sisko recounts his life, which has become an endless quest to locate his father, after an accident in the engine room of the Defiant apparently claimed Benjamin Sisko's life.

Believing that the recent Cardasssian coup was orchestrated by the Dominion, the Klingon decision to attack Cardassia puts the Federation-Klingon alliance in jeopardy, and forces Worf to choose between his people and his oath to the Federation.

When a Klingon fleet under General Martok arrives at the station ostensibly to protect the Alpha Quadrant from the Dominion, Sisko recruits Lieutenant Commander Worf to investigate the Klingons' true intentions.