The Search, Part I
Sisko returns to the station after a long debriefing at Star Fleet, newly promoted to Captain, and bringing with him the USS Defiant, a prototype ship designed to deal with the Borg menace, now reassigned to DS9 to help in the fight against the Dominion, and equipped with a cloaking device, loaned by the Romulan Empire. Sisko and the crew set off in the new ship to find the mysterious founders of the Dominion. All too soon they encounter the Jem'Hadar and Dax and O'Brien are captured.
The Search, Part II
While Odo comes to terms with an amazing discovery about his past, Kira attempts to contact Sisko and the others. Meantime Sisko returns to the station to discover that things are changing at an extremely fast rate; the more he discovers the more concerned he becomes. In the end, he decides to take matters into his own hands...
The House of Quark
After Quark accidentally kills a drunk Klingon in a brawl in his bar, Quark claims he fought the Klingon and won. His tall tale helps rebuild the dwindling clientele at his bar, and all seems to be going well until the family of the dead Klingon arrive on the Station. Soon Quark is kidnapped, taken back to the Klingon home world, and forced to marry the widow of the Klingon he killed. He then finds that he is embroiled in a bitter feud between two Klingon houses.
Dax starts suffering from a severe hallucinations and keeps on blacking out. Concerned, Sisko and Bashir take her back to the Trill homeworld where they hope to find an answer to her plight. Soon it becomes apparent that the Trill authorities are hiding something and are prepared to sacrifice Jadzia's life to stop the truth coming out.
Kira comes across a record that implies that she spent time in a Cardassian prisoner of war camp on Bajor, and when she investigates she discovers other people who were there claim to know her. She heads down to Bajor to investigate, but never reaches her destination. She wakes up to find herself on Cardassia, apparently a Cardassian and is told that she was a Cardassian spy who has been working on Bajor for the last ten years. She refuses to believe but they show her a range of evidence including apparently dead body of her truly Bajoran alterego. She appears to be the daughter of an important man, a Legate in the Cardassian senate.
Odo tries to convince a young, violent Jem'Hadar that there is more to life than fighting and killing.
A trapped crew fights to save the station from self-destruction when an automated Cardassian security program is accidentally activated.
Dax falls in love with a man who will soon disappear with his planet into another dimension for sixty years.
Will Riker's renegade duplicate, Tom Riker, steals the Defiant and attacks Cardassian territory, forcing Sisko to assist Gul Dukat in stopping him.
A Bajoran celebration on the station serves as the backdrop for an epidemic of inexplicable romantic attractions among the crew.
Past Tense, Part I
The command officers of Deep Space Nine return to Earth in the Defiant to brief Starfleet on the situation in the Gamma Quadrant. As Sisko, Bashir and Dax beam down something goes wrong with the transporter and they never arrive at Starfleet Headquarters. While O'Brien and Kira try to figure out where they went, Bashir and Sisko are arrested as vagrants outside a metro station in the year 2024. Dax is luckier and is rescued by a passer by and given assistance in obtaining credentials.
Past Tense, Part II
When Starfleet suddenly ceases to exist, Kira and O'Brien set off on journeys through time trying to recover Sisko, Bashir and Dax. Meantime, Sisko decides to pose as the dead man and becomes a major player in the riot ringleaders. However they soon find out just how difficult it is to follow the pre-ordained path needed to restore their version of the past, for in their history the leader of the rioters, Gabriel Bell, is shot in the final few minutes of the riot. Since Sisko is now posing as Bell, it is he who will have to die.
Bashir must use questionable methods in order to keep Vedek Bareil alive long enough to help bring about a Bajoran peace treaty with Cardassia.
Heart of Stone
A desperate situation that could cost Kira her life forces Odo to face the depth of his feelings for her.
Sisko ignores an ancient Bajoran prophecy of doom in order to undertake a joint scientific venture with the Cardassians.
When the Ferengi leader suddenly decides to abolish his race's greedy ways, Quark is determined to find out the truth behind his actions.
An accident causes O'Brien to inadvertently jump into the near future, where he witnesses his own death.
After an encounter with a dubious acquaintance of Quarks, Dr. Bashir finds himself trapped in a bizarre dreamworld where each member of the DS9 crew seems to play a role. He begins to age rapidly and realizes that he has to find the answer before he dies of old age.
In a parallel universe, Sisko must assume the role of his dead counterpart in order to save the mirror version of his late wife.
Garak's shop mysteriously explodes, launching Odo on an investigation to determine who is trying to kill the Cardassian exile -- and why.
The Die Is Cast
On the eve of a Romulan/Cardassian attack against the Dominion, Garak may have to prove his loyalty to his former mentor by eliminating Odo.
Sisko becomes obsessed with a Bajoran legend that describes ancient Bajoran spaceship that sailed on the solar winds and made it call the way to Cardassia. He sets out to build a replica of the ship, and once built, sets sail in it with the assistance of his son Jake. Things do not go quite as expected and a miscalculation results in an extraordinary discovery.
Quark receives a visit from the FCA, the all-powerful overseer of Ferengi business who places a seizure notice on his bar. Informed that the seizure is due to the illicit activities of his mother, Quark returns to his home planet to confront her. He discovers that she has broken the Ferengi law prohibiting females from earning a profit.
Kira is asked to go an help reclaim some farming equipment from her former comrades in the resistance who are refusing to release it. Once she gets there she discovers that their need is very genuine and a string of promises have been broken by Kai Winnís government. When Kai Winn sends the troops in, Kira decides to aid her comrades and finds herself once again a rebel on the run. Soon a minor civil war has erupted and the struggle is on to gain control of the Bajoran government by toppling Kai Winn.
It is Jadzia's time to meet her former hosts through a Trill ceremony where the personality of a former host takes over another person so that Jadzia can talk with them as a separate person. She selects Kira, O'Brien, Bashir, Quark, Leeta, Odo and Sisko as the hosts for her previous personas. All but Quark, readily accept and she manages pursued Quark in the end. the problems start when one of the past hosts refuses to give up it's new-found body and be returned to Jadzia.
A visiting ambassador briefs the command personnel on a coup d'etat within one of the Federations newer allies, a former enemy with whom a peace was only recently found. He recommends that they dispatch the Defiant as a show of Federation strength to ensure that the new government does not break the treaty. As they near the territory of the alien race, they realize that they have been tricked and that the Defiant is now under the control of one of Odo's race who is determined to start a war. Can they discover who the shape shifter is in time, or will Sisko have to destroy the Defiant in order to avoid war?