Stardate: Unknown Three months after the wormhole was sealed and the Bajoran Orbs became useless, Sisko must find the Bajoran Orb of the Emissary in order to re-open the wormhole and reactivate the Orbs. Kira, now in command of Deep Space Nine until Sisko returns, is informed that the Romulans wish to set up a station office and a hospital on a Bajoran moon. Sisko has visions of a woman's face buried in the sand, who is revealed to be Sisko's real mother. Sisko encounters the new host of the Dax symbiont, a young woman named Ezri.

Stardate: Unknown Worf attempts to win a battle by destroying a Dominion shipyard to guarantee Jadzia's spirit a place in Sto-vo-kor, the Klingon afterlife. Ezri wishes to join Ben, Joseph and Jake Sisko on their hunt for the Bajoran Orb of the Emissary. After discovering the Orb, and opening the case, the Wormhole is re-opened and the Orbs are reactivated. Sisko learns that a Prophet, to ensure his birth and guarantee his destiny, possessed his mother. Kira must find a way of preventing the Romulans from building weapons on the Bajoran moon where they claim they are building a hospital.

Stardate: Unknown On Deep Space Nine, Ezri must deal with the different reactions of the crew to her presence: Kira tries to be friendly, Quark flirts with her, Worf wants nothing to do with her, and Sisko is happy to see her. Ezri makes plans to leave the station due to Worf's discomfort around her presence, and the painful memories she provokes. When Garak collapses with terrifying bouts of claustrophobia, Sisko invites Ezri to stay aboard Deep Space Nine as the station's new counsellor.

Stardate: Unknown Sisko challenges an old Starfleet Academy acquaintance, the Vulcan Captain Solok, to a game of Baseball on the holosuite.

Stardate: Unknown A group of genetically enhanced humans appeal to Dr. Bashir to help cure their friend Sarina, who has mysteriously entered a catatonic state.

Stardate: Unknown Odo must get a cloned Weyoun, who wishes to defect, back to Deep Space Nine without their runabout being destroyed by Jem'Hadar troops. Odo also learns that a virus is slowly wiping out the changeling Founders.

Stardate: Unknown Worf grants Kor a place on his ship as they launch an attack against the Dominion. Tensions rise when Martok encounters Kor, who denied him officer status many years ago because Martok was descended from a common house.

Stardate: Unknown Sisko plans an attack that will allow them to tap in to the Dominion's communication array in the Alpha Quadrant on the planet AR-558. He must also find a way of revealing the 'Houdinis'; mines which hide themselves in subspace and explode without warning. Nog loses his leg during a battle.

Stardate: Unknown Dukat tries to persuade Kira to join a cult that worships the Pah-wraiths when she is unexpectedly transported to Empok Nor.

Stardate: Unknown Nog takes medical leave in the holosuite program of a 1962 Earth Las Vegas lounge after he lost his leg during a previous battle. Although his new leg is fully functional, he still uses a walking stick, a purely psychological situation, which one of the holo-characters, Vic Fontane, tries to help him overcome.

Stardate: Unknown Miles O'Brien disappears while on a secret trip to New Sydney, which is in a system where Ezri's mother owns a mining company. While on her journey, Ezri is reunited with her estranged family.

Stardate: Unknown Grand Nagus Zek is kidnapped by members of the resistance cells from the mirror universe. The mirror universe's Ezri arrives on Deep Space Nine and offers an exchange: a cloaking device for Zek. Quark and Rom accompany the Mirror Ezri back to her universe where they are captured and held prisoner.

Stardate: Unknown Ezri is enlisted to help track down a serial killer that is loose on Deep Space Nine. In order to gain an insight into the killer's mind, she calls on the experiences of self-professed murder and a past host of Dax, Joran.

Stardate: Unknown Odo meets another shapeshifter, whom he recognises as one of the 100 infants sent out to learn abouth other species and cultures. The changling, Laas, offers Odo the chance to join him and search for the rest of his kind that were sent out.

Stardate: Unknown The senior crew of Deep Space Nine takes on roles in the holosuite to save Vic Fontane's lounge from being controlled by mobsters.

Stardate: Unknown As Dr. Bashir leaves for a medical convention on Romulus, a member of Section 31, who asks him to get as much information on the Romulan Government as possible, approaches him. It soon becomes clear that Bashir may be caught in a confused double cross.

Stardate: 52576.2 Sisko buys land on Bajor. Worf goes missing, and Ezri steals a runabout to find him. Sisko proposes to Kasidy, but he is soon warned by the Sarah prophet to break the engagement.

Stardate: Unknown Dukat, surgically altered to look Bajoran, tries to gain Kai Winn's confidence. Sisko cancels his engagement with Kasidy, but shortly changes his mind and marries her despite further warning from the Sarah Prophet. The Breen join the Dominion/Cardassian Alliance.

Stardate: Unknown Ezri and Worf are taken aboard a Jem'Hadar ship where the Dominion/Breen treaty is signed. Ezri and Worf soon discover that they are to be put to death. Kasidy has a hard time adjusting to her new role as wife of the Emissary. Damar provides an escape route for Worf and Ezri just as they are lead to the execution chambers. Kai Winn decides to join Dukat in following the Pah-wraiths.

Stardate: Unknown Worf and Ezri return safely to Deep Space Nine. The Breen launch an attack on Federation Headquarters, while Damar secretly forms plans to free Cardassia from Dominion rule. Sisko is informed that the Breen have launched an attack against the only foothold the Federation has in Dominion territory. Kai Winn and Gul Dukat try to find a way of releasing the Pah-wraiths from the Fire Caves on Bajor.

Stardate: Unknown Sisko orders Kira to teach Damar and his troops resistance tactics. Bashir asks for Odo's help in searching for a cure to the virus that is slowly killing the Founders, when he discovers that Odo is also infected with it. Gowron overthrows Martok's command of Klingon forces. Kai Winn continues to search for a way of revealing the text in the Kosst Amojan, a sacred text that contains the secret of releasing the Pah-wraiths, if the writing can be revealed. Bashir suspects Section 31 of creating and releasing the Founder's virus.

Stardate: Unknown Bashir works around the clock to find a cure for the Founder's disease. Kira makes plans to steal Breen technology that would make the Federation ships immune to Breen/Dominion weaponry. Damar learns that his family was killed by the Dominion. Worf challenges Gowron's corrupt leadership of the Klingon Empire, which results in Gowron's death. Bashir and O'Brien plot to capture a member of Section 31 who may hold the cure for Odo's illness.

Stardate: 52645.2 O'Brien and Bashir manage to lure Sloan, the Section 31 operative, to Deep Space Nine where they probe his mind and enter his consciousness to find a cure for the virus plaguing the Founders, as well as Odo.

Stardate: 52861.3 Sisko takes command of a new ship named in honor of the Defiant, while Kira, Garak and Damar barely survive a Dominion ambush on Cardassia Prime. Bashir and Ezri reveal their attractions for one another over coffee. Quark is appointed Zek's successor, and he is determined to overthrow new democratic changes that have just been implemented into Ferengi society. Garak, Damar and Kira successfully plant a bomb in Dominion barracks on Cardassia. In a shock turn of events, Zek appoints Rom as the new Grand Nagus of Ferenginar, despite Quark's earlier announcement.

Stardate: Unknown Sisko launches the Federation/Klingon/Romulan attack against the Dominion on Cardassia. Kira, Damar and Garak destroy a power supply on Cardassia as the Cardassian population rises against the Dominion. Kai Winn asks Gul Dukat to join her in releasing the Pah-wraiths from the Fire Caves. Bashir and Ezri spend the night together on the eve of the war. The Founder Leader orders the execution of Damar, Garak and Kira after Jem'Hadar forces capture them; however, Cardassian forces free them. Meanwhile, on Bajor, Kai Winn recites from the Kosst Amojan in an attempt to release the Pah-wraiths.

Stardate: Unknown The war turns in favour of the Federation/Klingon/Romulan forces as the Cardassians change sides mid-battle. In retaliation, the Founder Leader orders the extermination of the Cardassian race. Kira, Garak and Damar take over the Dominion briefing room, where Garak kills Weyoun and Kira hold the Founder Leader at gunpoint, ordering her to stop the war and surrender. Kira contacts Sisko, who orders Odo to link with the Founder Leader. He does so, and cures her of the virus that has ravaged her people. In light of this event, she calls a cease-fire. Odo tells Kira that he is returning to his homeworld. In the Fire Caves on Bajor, Kai Winn offers Dukat as a sacrifice to the Pah-wraiths. With the signing of the surrender documents, the war officially ends. Later, O'Brien announces that he is returning to Earth with his family to teach at Starfleet Academy, Odo makes plans to return to his homeworld to heal the other Founders, and Worf is appointed Federation Ambassador to