Stardate: 49011.4. When the Klingons bring a task force to DS9, Captain Sisko sends for Starfleet's lone Klingon officer, Worf, to uncover the mysterious intentions of their presence.
Stardate: Unknown. Melanie, an aspiring writer, wants to know why Jake Sisko stopped writing at 40. Jake tells how his father died in an accident and then suddenly reappeared.
Stardate: 49066.5. Bashir is asked to help a group of renegade Jem'Hadar break their addiction to ketracel white. Meanwhile Worf is dissatisfied with the way Odo runs security.
Bashir is captured, with Chief O'Brien, by a rogue group of Jem'Hadar who are attempting to overcome their genetic addiction to Ketracel White. Their leader, Goran'Agar, is able to survive without it and forces Bashir to find out why. Worf is finding it difficult to leave security matters to Security Chief Odo.
Forced to bring along Dukat on a personal mission to investigate the fate of the Cardassian prison ship Ravinok, which disappeared six years ago, Kira discovers the real reason her old enemy wants to accompany her. Sisko appears to have reservations about Kasidy Yates' coming to live on the station.
Dax is reunited with Lenara Kahn, whose previous host was the wife of one of Dax's former hosts, Torias Dax, and the two struggle with their feelings for one another.
Stardate: Unknown. Quark and Rom take Nog to Earth and Starfleet Academy, but a malfunction with the ship takes the crew back in time, to Roswell New Mexico in 1947.
The USS Defiant becomes trapped in the atmosphere of a gas giant while battling with the Jem'Hadar.
Stardate: Unknown. When an transporter emergency turns the command crew into holosuite characters, Bashir's James Bond fantasy takes on a deadly reality.
Bashir plays a 1960s secret agent in a holosuite, when Garak unexpectedly intrudes, but his help is needed when the DS9 computer uses the holosuite to store the patterns of other crew members during a transporter accident.
Stardate: Unknown. When Starfleet institutes martial law to combat the Changeling Menace, Sisko begins to question if the Dominion is the real threat.
As Sisko and Odo prepare for a Dominion invasion, they discover a plot to place the Federation under military control. (Part 2 of 2)
Stardate: Unknown. Dukat returns, stripped of his prestige, to escort Kira to a Cardassian conference about the Dominion. But an attack by a Klingon raider may give Dukat a chance to redeem himself in the eyes of his government.
Stardate: 49556.2. Worf's brother Kurn asks him to perform a death rite to regain his lost honor. Meanwhile Kira and O'Brien investigate Klingon activity near the Bajoran border.
Cast out of Klingon society because of Worf's dishonor, his brother, Kurn, asks Worf to kill him. Kira and O'Brien investigate a mysterious high-energy discharge just outside Bajoran space.
After he nearly dies because his contract kept him from seeking medical help, Rom organizes the Guild of Restaurant and Casino employees, a union for Quark's downtrodden staff, and they go on strike when their demands for fairer treatment are rejected.
A famous Bajoran poet, Akorem Laan, who disappeared over 200 years ago, appears from the wormhole and convinces Sisko that he is the true Emissary, but when he announces a return to the pre-occupation caste system, Sisko points out it would disqualify Bajor for membership in The Federation. O'Brien is less than enthusiastic when Keiko announces she's expecting.
Worf accidentally destroys a civilian ship during battle and faces a hearing to determine whether he should be extradited to the Klingon Empire.
Stardate: Unknown. When the Mirror Universe counterpart of Sisko's deceased wife lures Jake to the other side, Sisko must follow and help the human resistance against the Alliance's forces.
Stardate: Unknown. A mysterious woman approaches Jake about his future as a writer. Odo promises to do whatever it takes to help Lwaxana Troi keep her baby over the father's wishes - even if it means marrying her himself.
Stardate: Unknown. Sisko must face betrayal when evidence surfaces that Kasidy is smuggling for the Maquis. Meanwhile Garak makes acquaintance with Ziyal.
Stardate: 49904.2. A renegade group of Jem'Hadar plunders Deep Space Nine. Sisko agrees to a combat operation with loyal Jem'Hadar to prevent the renegades completing a planetary gateway.
Sisko and the Defiant crew join forces with the Jem'Hadar to stop a group of Jem'Hadar renegades from gaining power using an Iconian Gateway discovered in the Gamma Quadrant.
Bashir tries to free the population of a Gamma Quadrant world in the Teplan system of an engineered disease left by the Dominion 200 years previously.
Quark is diagnosed with a terminal disease, Dorek's Syndrome, and given a week to live. Due to an unavoidable accident on the runabout Volga, Miles and Keiko's unborn baby is transferred to Major Kira by Dr. Bashir.