While Kira welcomes a Romulan presence to the Bajoran system, Sisko has a vision telling him how to re-establish contact with the Prohets, and Dax returns in a new host body.

Worf, Quark and Bashir embark on a dangerous mission to win a place for Jadzia in Sto-Vo-Kor. While Kira reacts to a discovery of Romulan armaments, Sisko locates the Orb of the Emissary.

Confused by her new situation and the reactions of those around her, Ezri Dax plans to leave DS9, but is given a mission to complete first to counsel the moody and antagonistic Garak.

An ultra-competitive Vulcan captain whol Sisko has disliked for years arrives at DS9, and Ben cannot resist fuelling the rivalry by accepting a challenge to a baseball match. Solok's Logicians vs the Deep Space Niners.

The group of genetically engineered savants returns to DS9, seeking Bashir's help to cure the catatonic Sarina. Although the doctor is able to help his friend, his ministrations cause unforseen complications in Sarina's development.

Tricked into a meeting with Weyoun, Odo is stunned to hear that the Vorta wishes to defect. Pursued by Dominion forces determined to kill the traitor, Odo receives some crucial information.

To the annoyance of General Martok, Worf appoints ageing Klingon Commander Kro to a position on Martok's flagship. When Worf and Martok are knocked out, Kor takes command and nearly destroys the Ch'Tang.

Assisting in the defence of an imprtant communications array, Sisko's team join forces with a Starfleet unit which has already suffered heavy casualties, ans one of Sisko's team loses a limb.

Transported to Empok Nor, Kira is shocked to find Dukat leading a religious cult that worships the Pah-wraiths. To avoid exposure as a fake, Dukat intends to murder his followers in a "mass suicide".

After losing his leg in battle, Nog has difficulty accepting his synthetic leg and withdraws from reality to the holographic Las Vegas lounge of Vic Fontaine.

When O'Brien disappears on a secret trip to New Sydney, Sisko despatches Ezri to use her mother's mining operation as a base while she helps to find the Chief. O'Brien's investigation leads to dark secrets in Ezri's mother's business.

On a business trip to the Mirror universe, Grand Nagus Zek is kidnapped and will be killed unless Quark can secure a cloaking device for a starship. Quark's initial success soon goes badly awry.

To find a serial killer who is preying on Starfleet officers using an experimental weapon, Ezri summons one of Dax's former hosts, and finds the murderous Joran Dax difficult to control.

Odo's ship is tracked and boarded by Laas, a shapeshifter who was one of the "hundred" changelings originally sent out by the Founders. Unfortunately, Laas distrusts humanoids and kills a Klingon, inviting retribution.

Distressed when Voc Fontaine's club is usurped by mobster Frankie Eyes, but unable to edit the new character out of the program, the DS9 crew stage a casino heist to get Frankie's superiors to remove him.

Section 31 instructs Bashir to diagnose whether a senior Romulan official is suffering from a dangerous disease, Although Bashir fears that the information will be used to eliminate the Romulan, his superiors direct him to play along.

While Ezri Dax searches for the missing Worf, Sisko plans his marriage to Kasidy Yates, and is abruptly warned off by the Prophets. On Cardassia, Gul Dukat's plans and appearance take a bizarre turn.

Having called off his wedding, Sisko again proposes to Kasidy, promising not to change his mind. Dukat, disguised as a Bajoran, courts Kai Winn, and Worf and Ezri, tortured by the Breen, witness a historic alliance.

Facing execution by the Breen, Worf and Ezri examine their feelings for one another, while Damar grows increasingly suspicious of his new allies. On DS9, Dukat attempts to persuade Kai Winn to champion the Pah-wraiths.

While Damar plots to free Cardassia, the Federation loses its foothold at Chin'toka, and the Defiant is destroyed. Meanwhile, Dukat and Kai Winn's evil plans proceed with the murder of a humble Bajoran.

Kira teaches terrorist tactics to Cardassian rebels while Martok questions Chancellor Gowron's strategy. Bashir suspects Section 31 of creating the Founder's disease from which Odo now suffers, and a blind Dukat is ejected by Kai Winn.

While Worf advises Martok to challenge his Chancellor's authority, Kira and the Cardassian rebels attempt to steal powerful Breen technology. Bashir's unsuccessful attempts to cure Odo lead to a plot to dupe Section 31.

To cure a terminally ill Odo, Bashir and O'Brien lure Sectio 31 operative Sloan to DS9. When Sloan attempts suicide during interrogation, Bashir and O'Brien link minds and enter his fading consciousness to retrieve the cure.

When Weyoun publicly announces Damar's death, Kira sees the chance to create a legend behind which Cardassia can rally. Meanwhile, Quark believes he has been named as the new Grand Nagus.

As the final space battle begins, Dominion atrocities on Cardassia provoke a revolt, Dukat and Winn attempt to release the Pah-wraiths from the Fire Caves of Bajor.

While Sisko, Ross and Martok plan a final assault in space, Kira and Garak lead the Cardassian resistance on the ground into Dominion headquarters and overtake the Briefing Room. Kira orders the Female Shapeshifter to surrender, but she refuses; soon after, the defiant Weyoun is killed by Garak.

When Kira alerts Sisko to the situation on Cardassia, Odo asks to meet with the Female Shapeshifter. In the Fire Caves, Winn poisons Dukat with a glass of wine — and presents his body as a religious sacrifice to the Pah-wraiths. Hoping to commune with the Female Shapeshifter, Odo links with her and heals the Shapeshifter of the disease that has ravaged their people. Transformed by the experience, she orders a cease-fire. Eager to cure the rest of the ailing Shapeshifters, Odo informs a deeply saddened Kira that he is returning to his homeworld.

With the signing of surrender documents, the war officially ends. Later, Worf agrees to become the Federation Ambassador to Kronos and O'Brien announces that he's returning to Earth to teach. The crew holds a farewell party for Worf, O'Brien and Odo. Meanwhile, the Pah-wraiths bring Dukat, as a Cardassian, back to life in the Fire caves, and Sisko abruptly leaves the party — after a vision from the Sarah Prophet — to visit the site. Sisko confronts Dukat, and Winn is sacrificed to the Pah-wraiths; Sisko tackles Dukat and, along with the text of the evil Kosst Amojan, they plunge into the fiery abyss. Sisko "awakes" in a great vision: the Sarah Prophet assures him that he has completed his task by returning the Pah-wraiths to the Fire Caves; she then informs Sisko that he must now join the Prophets.

Back on the space station, Kasidy has a vision of Sisko in which he explains his reason for remaining with the Prophets — and he promises to return someday. In the meantime, Jake Sisko grapples with his father's departure; Bashir and O'Brien bid a fond farewell; Ezri Dax says goodbye to Worf; and Kira leaves Odo on the Changeling planet where a sea of ailing Shapeshifters awaits his curative link. At Deep Space Nine, Kira takes command of the Captain's chair, Ezri and Bashir plan their future, and, despite her own feelings of loss, Kira reaches out to comfort a fatherless Jake.