Three months into the war, DS9 is still under Dominion control. Sisko and his crew are given a mission to destroy a vital Ketracel White facility deep in Dominion space using a captured Jem'Hadar ship. Jake is working for the Federation News Service. Odo is head of Terok Nor's security supported by the Vorta Weyoun.
Stardate: Unknown. Sisko and his crew are marooned on a barren planet with a squadron of Jem'Hadar soldiers and their wounded Vorta overseer. But when the Vorta seeks out Sisko to make a deal, can he be trusted? And should Sisko accept the treacherous proposal?
Stardate: Unknown. Worf and his son Alexander must come to terms with one another when Alexander is assigned to the Rotarran and voices his intentions to become a warrior. Meanwhile, Kira finds herself between friend and foe when Ziyal returns to the station and reconciles with her father.
Sisko creates a risky plan to disable a critical Dominion sensor array able to see five sectors out, while on Terok Nor, Kira, Jake, Rom and Odo seek to undermine the Cardassian/Dominion Alliance.
Learning of thousands of Dominion reinforcements gathering in the Gamma Quadrant, Sisko initiates a plan to retake Deep Space Nine and secure the wormhole before the minefield is detonated. (Part 1 of 2)
Sisko commands the Defiant and 600 Federation ships against a Dominion/Cardassian armada to retake Deep Space Nine. Damar has Kira, Jake and Leeta arrested. (Part 2 of 2)
Worf's plans for a traditional Klingon wedding hinge on Martok's demanding wife, Sirella, accepting Dax into their family.
The Mirror Universe counterpart of Kira's dead love, Vedek Bareil, takes her hostage on Deep Space Nine as he is running from the evil Alliance of his universe.
Bashir attempts to reintegrate genetically engineered misfits into society, but they are asked by Starfleet to become a think tank when they provide insightful analysis of upcoming Dominion peace talks.
Quark mounts a rescue mission when his mother, Ishka, is captured by the Dominion and Grand Nagus Zek offers a reward for her return.
An attack on the Starfleet ship carrying Gul Dukat to a hearing for war crimes, as well as Captain Sisko who is to testify at the hearing, leaves the two of them stranded on a deserted planet together.
Morn is killed in an ion storm and Sisko informs Quark that Morn left his entire estate to him. But Quark has a little competition.
As Sisko considers leaving Starfleet due to the destruction of Captain Swofford's ship, the Cortez, he has a vision of himself as a science fiction writer in the 1950s.
Stardate: 51474.2. An attack by the Dominion on Sisko's ship endangers Dax and her crew aboard as she leads them into an anomaly that shrinks them to a very minute size. Unfortunately, they were being held stable by Sisko within a tractor beam, which was discontinued during the attack.
Starfleet Intelligence recruits Chief O'Brien to infiltrate the Orion Syndicate to find a Starfleet informant.
Stardate: 51597.2. Worf and Jadzia travel to the badlands to procure some information on the Dominion from a traitorous Cardassian. Bashir wants to engage in a holo-suite spy simulation, but O'Brien prefers to brush up on his tongo game after watching Jadzia lose to Quark.
Stardate: Unknown. After receiving some disturbing information from Gul Dukat, Major Kira seeks Sisko's approval as Emissary to travel back in time to find out the truth about her mother. Meanwhile, Chief O'Brien and Dr. Bashir discuss a holosuite program surrounding the Battle of the Alamo.
Dr Bashir is busy wrapping up unfinished tasks prior to departing DS9 to attend a medical conference. Just prior to his departure, an Internal Affairs unit under the command of an individual named Sloan, arrive and announce they will be interviewing all the senior staff. Things take a worrying turn for the good doctor when he realises that he is the subject of the investigation and Sloan accuses him of spying for the Dominion.
Weary of posting yet another weekly casualty list, Captain Sisko becomes determined to get the Romulans to join the war against the Dominion. He seeks the shady expertise of Garak to help achieve his objective. But the bloody reality of the phrase “whatever it takes”, soon finds Sisko’s ethics being compromised to breaking point in pursuit of his goal.
Bashir shows off a new Holosuite program of a martini lounge with a 1960s Vegas singer named Vic Fontaine who is very perceptive; and gives advice to Odo when Kira visits her ex-lover Shakaar.
Stardate: Unknown. Sisko runs afoul of Kai Winn when he removes a Bajoran artifact from an archaeological dig after he receives a vision from the Prophets.
Jake and Nog come under attack by the Jem'Hadar and are rescued by a rogue Defiant class starship, the Valiant, under the command of Starfleet Red Squadron cadets.
Stardate: Unknown. Quark's mother and the Grand Nagus show up on DS9, announcing a new amendment to the Bill of Opportunities he has instituted on the home planet of Ferenganar, and then follows up with the announcement, that, due to the new amendment, chaos has followed and he has been deposed.
Molly O'Brien disappears in a vortex and reappears as an 18-year-old woman, but she is now feral, bringing great difficulty for her parents.
The Defiant picks up a distress call from Captain Lisa Cusak, whose escape pod has crashed on a remote planet following the destruction of her ship, the Olympia.
Starfleet Command begins an offensive against the Dominion, and Sisko is chosen to lead the invasion of Cardassia, but the Cardassian/Dominion Alliance has secretly reinforced their borders with unmanned orbital weapons platforms.