With continuing convoys of Jem'Hadar arriving in the Alpha Quadrant, Sisko decides to mine the wormhole to prevent further troop movement. However, this decision forces the Federation into a direct confrontation with the Dominion, and Gul Dukat responds by launching a massive assault fleet against DS9.

Jake and Nog go through hell and high water while trying to cheer up the war-fatigued Captain Sisko by acquiring a mint-condition 1951 Willie Mays baseball card. Meanwhile, Weyoun arrives on DS9 to meet with Kai Winn and offers to sign a nonaggression pact with Bajor.

While salvaging components from DS9's sister station, Empok Nor, the crew run afoul of a disturbing surprise left behind by the Cardassians.

Driven to desperation by the Dominion, the Maquis launch a massive strike against Cardassia. In order to prevent mass Cardassian casualities, Sisko is forced to trust the traitor Michael Eddington to try to stop the missiles from reaching their target.

Investigating an isolated planet surrounded by a powerful energy field, the crew of the Defiant discovers the unexpected history of the planet's colonists.

Dax and Worf accompany Martok on his first command since being held by the Dominion. But the ship they are given hasn't seen victory in months and the crew is near mutinous, forcing Worf to decide between loyalty to his commander and loyalty to his crew.

Feeling depressed, Quark returns home to Ferenginar to visit his mother, but doesn't know whether to be panicked or overjoyed when he learns that she is now the secret lover of the Grand Nagus.

Takeny Ghemor, who considers Kira to be his daughter, arrives on DS9 and confesses that is dying. Ghemor wishes to commence the Shri-tal with Kira, a Cardassian ritual in which a dying person reveals their closest secrets to the rest of the family. But the experience dredges up Kira's memories of her own father, who suffered a fatal injury during the Occupation of Bajor.

Quark must wrestle with his conscience when his cousin Gaila offers him a lucrative job as a weapons dealer.

Odo falls for a mysterious woman who has been targeted for murder by the Orion Syndicate.

Dr. Lewis Zimmerman arrives on DS9 intending to use Dr. Julian Bashir as the model for his new Long-term Medical Hologram, but when Zimmerman's plans threaten to unveil a dark secret that Bashir has carried since childhood, Julian is forced to make a life-altering confession.

The crew of DS9 prepares to defend the Alpha Quadrant from an invading Dominion fleet. Still trapped in the Gamma Quadrant, Worf, Garak, and the other prisoners continue their attempts to escape from the Dominion Internment Camp.

Garak and Worf investigate a coded message which suggests that Garak's mentor, Enabran Tain, is still alive in the Gamma Quadrant. However, when their search for answers leads them into Dominion space, the pair discover something far worse than they had expected.

Sisko obsessively pursues the former Starfleet officer Michael Eddington, now the leader of the Maquis.

The discovery of an infant Changeling gives Odo a chance to correct what he sees as the invasive mistakes in his upbringing. Meanwhile, Kira goes into labor with the O'Briens' baby.

Major Kira is forced to confront her actions during the Cardassian Occupation when a mysterious assassin begins killing members of her former resistance cell.

On the eve of Bajor's entry into the Federation, Sisko begins experiencing visions that lead him to ruins of the lost Bajoran city of B'hala. However, when the visions that are guiding him become potentially fatal, Sisko must choose between his faith in the Prophets or his life.

Quark and Odo are forced to put their grievances aside when they crash land on an inhospitable planet and must work together to survive. Back on DS9, Nog returns from Starfleet Academy and moves into new quarters with Jake.

Sisko, Dax, Odo, and Garak find themselves trapped seven years in the past on Terok Nor, but everyone thinks that they're condemned Bajorans. With Cardassians in control of the station, Odo's memory of a crime he once investigated may be the only key to their survival.

After agreeing to vacation on Risa with Jadzia, Worf is irritated to discover they will be joined by Dr. Bashir, Leeta, and Quark. However, everyone's vacation is thrown into disarray by the arrival of a radical fundamentalist group determined to start a political revolution on Risa.

When Temporal Investigations arrives on DS9, Sisko recounts how he and the crew of the Defiant traveled back in time to prevent the assassination of Captain James T. Kirk during the original Enterprise's mission to Space Station K-7.

Keiko O'Brien returns from the Fire Caves on Bajor possessed by an alien entity which demands that Chief O'Brien follow its every instruction if he doesn't want his wife to die.

On their way back from a medical conference, Jake and Dr. Bashir are diverted to the Federation colony on Ajilon Prime who have been attacked by the Klingons. However, when the the Klingons renew their attacks on the colony, Jake is forced to confront the hard realities of war as battle erupts around him.

When Grilka, Quark's ex-wife, unexpectedly visits DS9, Quark asks an already smitten Worf to help him pursue his former wife. Elsewhere, O'Brien and Kira struggle with their feelings for each other now that Kira is carrying the O'Brien's unborn child.

While conducting a a mineral survey of an uninhabited planet in the Gamma Quadrant, the crew of the Defiant encounter a crashed Jem'Hadar ship and must fight to get it, and themselves, back to the Federation.

As the war between the Federation and the Klingon Empire intensifies, Sisko leads an undercover team deep into Klingon territory in an attempt to expose the Changeling impersonating Chancellor Gowron.