Season six begins with the Confederation losing the war. The Jem'Hadar ship crashes, leaving Dax injured and under the care of Dr. Bashir. Sisko has been promoted and Dax is put in command of the Defiant. Worf must decide between the life of his wife Jadzia, and the success of his mission. OthQuark's relationship with Rom's mother, Ishka, convinces Grand Nagus Zek to allow equal rights for women. Sisko has been ordered to launch attacks against Cardassia and the Dominion.
Several months after Deep Space Nine was handed over to the Dominion, the Federation is losing the war.
The damaged Jem'Hadar ship crashes on a planet. Dax is seriously injured, but kept alive by Dr. Bashir. A group of Jem'Hadar who also crashed on the planet finds them...
Worf must help his son, Alexander, to learn the ways of a Klingon warrior, while on a ship patrolling for Dominion vessels.
Sisko is promoted, and Dax is placed in command of the Defiant. Meanwhile, on Deep Space Nine, now named Terok Nor, Kira must find a way of preventing the minefield from being destroyed.
Odo struggles with his choices between his friends and the Link. Sisko faces a suicide mission in order to reclaim Deep Space Nine.
Sisko faces thousands of Dominion warships alone in an attempt to regain Deep Space Nine.
Worf and Dax's marriage is threatened when Martok's wife does not welcome Dax into the House of Martok.
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.
By orders of the Grand Negus Zek, Quark enlists the help of Rom, Nog, his cousin Gaila, a Ferengi assassin named Leck, and Brunt to attempt to rescue his mother.
While en route to Gul Dukat's war crimes hearing, the ship carrying them is attacked. Dukat escapes with an injured Sisko and they crash on a planet...
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.
Sisko has visions of himself and his crew as writers for a science fiction paper in 1950's Earth.
Dax, O'Brien, and Bashir take the Runabout Rubicon to explore a nebula, where the runabout and its contents shrink to less than 1% of their original size.
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.
Worf is forced to choose between the life of his wife Jadzia, and the success of the mission...
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.
Bashir falls under suspicion of unknowingly supplying information to the Dominion, however, all is not as it may seem...
Sisko and Garak lure the Romulans into the Dominion war in order to get them to join the Federation/Klingon Alliance.
Odo uses Bashir's holosuite character of Vic Fontaine to bring himself and Kira closer together.
A mysterious tablet is found in the ruins of B'hala, foretelling that "The Reckoning" will soon begin.
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.
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.
While on a nearby planet, the O'Brien family picnic is interrupted when Molly wanders off and falls into a vortex that sends her 300 years into the past.
The Defiant attempts to rescue Captain Lisa Cusak who has crashed on a planet with high amounts of carbon dioxide, with a limited supply of triox to keep her alive. Meanwhile on the station, Quark attempts to keep Odo distracted while planning an illegal transaction.
Sisko is ordered to launch attacks against Cardassia and the Dominion. In his absence, Dax is left in command of the station.