- The Search, Part 1
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 gunship 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 2
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
In order to boost his business and gain respect, Quark lies about killing a Klingon, then winds up forced to marry the dead man's widow.
- Equilibrium
- Second Skin
Kira is kidnapped by the Cardassians, who try to prove to her that she is really one of their people.
- The Abandoned
Odo tries to convince a young, violent Jem'Hadar that there is more to life than fighting and killing.
- Civil Defense
A trapped crew fights to save the station from self-destruction when an automated Cardassian security program is accidently activated.
- Meridian
Dax falls in love with a man who will soon disappear with his planet into another dimension for sixty years.
- Defiant
Riker's renegade duplicate steals the Defiant and attacks Cardassian territory, forcing Sisko to assist Gul Dukat in stopping him.
- Fascination
A Bajoran celebration on the station serves as the backdrop for an epidemic of inexplicable romantic attractions among the crew.
- Past Tense, Part 1
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. Bashir and Sisko are taken to a compound where the unemployed and mentally ill are kept, only to realise that they've arrived at the location of a famous riot only a few days before it's due to start. Things take a turn for the worse when the man due to be the ringleader of the riot is stabbed while trying to stop Sisko and Bashir being attacked.
- Past Tense, Part 2
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 possing as Bell, it is he who will have to die.
- Life Support
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.
- Destiny
Sisko ignores an ancient Bajoran prophecy of doom in order to undertake a joint scientific venture with the Cardassians
- Prophet Motive
When the Ferengi leader suddenly decides to abolish his race's greedy ways, Quark is determined to find out the truth behind his actions.
- Visionary
An accident causes O'Brien to inadvertently jump into the near future, where he witnesses his own death... and worse.
- Distant Voices
After an encounter with a dubious acquaintance of Quarks, Dr. Bashir finds himself trapped in a bizzare dreamworld where each member of the DS9 crew seems to play a role. He begins to age rapidly and realises that he has to find the answer before he dies of old age.
- Through the Looking Glass
In a parallel universe, Sisko must assume the role of his dead counterpart in order to save the mirror version of his late wife.
- Improbable Cause
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.
- Explorers
- Family Business
Quark returns to his home planet to confront his mother, who has broken the Ferengi law prohibiting females from earning a profit.
- Shakaar
Sent to Bajor on a mission against her former leader in the resistance movement, Kira ends up joining him as a fugitive.
- Facets
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, Leda, Odo and Sisko as the hosts for her previous personas. All but Quark, readily accept and she
manages to persuade 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.
- The Adversary
One of Odo's people tricks Sisko and the crew into actions that could start a war in the Alpha Quadrant.