Stardate: 51107.2 The damaged Jem'Hadar ship captained by Sisko crashes on a planet. Dax is seriously injured, but kept alive by Dr. Bashir. A group of Jem'Hadar who also crashed on the ship finds them, and takes them to their injured Vorta leader, who has a proposition for Sisko he may not be able to refuse.

Stardate: Unknown Worf must help his son, Alexander, to learn the ways of a Klingon warrior, while on a ship patrolling for Dominion vessels.

Stardate: 51149.5 Sisko is promoted, and Dax is placed in command of the Defiant. She must disable a Dominion sensor array that has been monitoring all traffic within five sectors. Meanwhile, on Deep Space Nine, now named Terok Nor, Kira must find a way of preventing the minefield from being destroyed. Odo's loyalties are questioned when he physically joins with the Founder Leader.

Stardate: Unknown Odo struggles with his choices between his friends and the link. Sisko faces a suicide mission in order to reclaim Deep Space Nine. Rom is ordered to be executed. Ziyal is assaulted by Damar - Kira sees this altercation and nearly kills Damar over it.

Stardate: Unknown Captain Sisko and his taskforce engage the Dominion as Starfleet pushes to reclaim DS9. Meanwhile on the station, the Dominion tries to complete its plan for removing the mines from the wormhole, and meet internal resistance.

Stardate: 51247.5 Worf and Dax's marriage is threatened when Martok's wife does not welcome Dax into the House of Martok.

Stardate: Unknown The mirror universe's Bareil attempts to steal the Bajoran orb of Prophecy and Change. Things are complicated when Kira falls in love with him.

Bashir is asked to help a group of genetically enhanced people integrate into normal society, but working around their personality problems. Soon, they must analyze a proposed treaty with the Dominion and predict its outcome.

Stardate: Unknown Quark enlists the help of Rom, Nog and his employees Gaila, Leck and Brunt to rescue his mother from a Dominion prison.

Stardate: Unknown It is announced that Morn has died and has left his entire estate to Quark. But claiming his inheritance lands him in a web of lies and deceit over the nature of Morn's wealth.

Stardate: Unknown Sisko has visions of himself and his crew as writers for a science fiction paper in 1950's Earth.

Stardate: 51474.2 O'Brien is ordered to infiltrate the Orion Syndicate to expose a Federation informant. However, his involvement may lead to the death of his new friend.

Stardate: Unknown When Gul Dukat reveals to Major Kira that her mother was a 'comfort woman' for him during the occupation, Kira uses the Bajoran Orb of Time to travel to the past and find the truth.

Stardate: 51721.3 Sisko and Garak lure the Romulans into the Dominion war in order to get them to join the Federation/Klingon Alliance. Without them, the Federation and Klingon Empire would eventually lose the war and fall under Dominion rule.

Stardate: Unknown A mysterious tablet is found in the ruins of B'hala, foretelling that "The Reckoning" will soon begin. As Sisko tries to translate the texts on the tablet, Kai Winn pays a visit to Deep Space Nine, demanding that the tablet should be given back to Bajor. Sisko, getting an impulse from the Prophets, smashes the tablet, releasing strange energy-beings. Subsequentely, a Prophet saying that she must defeat the 'Evil One,' which will then usher in Bajor's Golden Age, possesses Kira. Sisko does not intervene, even when the 'Evil One' inhabits the body of his son, Jake.

Stardate: Unknown Nog and Jake are rescued by the U.S.S. Valiant when their ship is attacked by the Dominion while on their way to Ferenginar. The crew of the Valiant consists of the Starfleet Cadet corps known as 'Red Squad,' an elite band of cadets, after the main crew were killed when the Dominion War broke out. They decide to complete their mission, which Jake sees as suicide.

Stardate: Unknown Thanks to his relationship with Quark and Rom's mother Ishka, Grand Nagus Zek announces that he will allow equal rights for women on Ferenginar. When Ishka has a heart attack, Quark poses as a convincing female in order to let the law pass.

Stardate: Unknown Sisko is ordered to launch attacks against Cardassia and the Dominion. In his absence, Dax is left in command if the station. Gul Dukat is possessed by a Pah-wraith in an attempt to destroy the Bajoran Wormhole and the Prophets. Dukat manages to destroy one of the Bajoran Orbs, and kills Jadzia in the process, although the Dax symbiont is saved. The Bajoran Wormhole implodes, the Orbs go dark, and Sisko is forced to take time out while the war continues.