First aired in 1998/1999.
- Image in the Sand
Captain Sisko attempts to re-establish contact with the Bajoran prophets, and learns the truth about his mother.
- Shadows and Symbols
Captain Sisko searches for the Orb of the Emissary.
Ezri Dax helps Garak with his claustrophobia, and attempts to readjust to station life as a new host.
- Take Me Out to the Holosuite
Captain Sisko's rival from his academy days comes to DS9 to challenge him and his senior staff to a game of baseball on the holosuite.
Doctor Bashir helps the genetically engineered Sarina come out of her cataleptic state.
- Treachery, Faith, and the Great River
Odo helps Weyoun 6 defect from the Dominion. Chief O'Brien trusts his access code to Nog, to get a new gravity net for the Defiant.
- Once More Unto the Breach
Martok's enemy Kor comes to the station and asks Worf to get him a battle assignment.
- The Siege of AR-558
The crew of the Defiant help defend a Federation outpost from Jem'hadar attack.
Gul Dukat takes Major Kira to Empok Nor where he has started a cult that worships the Pah Wraiths.
- It's Only a Paper Moon
Nog returns to DS9 after the events of AR-558 but has trouble re-adjusting to station life.
- Prodigal Daughter
Ezri returns to her family on the Trill homeworld to get help finding Chief O'Brien's missing friend.
- The Emperor's New Cloak
The Grand Negas is kidnapped and taken to the mirror universe. Quark and Rom must get him back by retrieving a cloaking device for the Alliance.
- Field of Fire
An unknown serial killer begins assassinating DS9 crew members at random. Ezri must call on the experience of her previous host Joran to solve the crime.
Odo and Chief O'Brien encounter another changeling, who attempts to convince Odo to explore the galaxy with him.
- Badda-Bing, Badda-Bang
When a jack-in-the-box is activated within the Vic Fontaine program on DS9, the crew must pull of an intricate casino heist to restore Vic's bar to its original state.
- Inter Arma Enim Silent Leges
Section 31 operative Sloan goes with Doctor Bashir on a mission to Romulas.
Captain Sisko receives a vision from the Bajoran prophets telling him to not marry Kasidy. Ezri defies orders to look for Worf, who had been declared missing after a dangerous mission.
- Til Death Do Us Part
Ezri and Worf are captured and interrogated by the Breen.
- Strange Bedfellows
The Breen allies with the Dominion in their war on the Alpha Quadrant.
- The Changing Face of Evil
The Breen launch an attack on Earth. Kai Winn begins reading ancient Bajoran texts about the Pah Wraiths.
- When It Rains...
Doctor Bashir finds out that Odo is infected with the same disease as the founders. Major Kira and Odo are sent to Cardassia to help Damar with his rebellion against the Dominion.
- Tacking Into the Wind
Chancellor Gowron assumes command of all Klingon forces, and begins sending them on foolish offensives against the Dominion. Kira and the Cardassian resistance attempt to steal a new weapon from the Breen.
- Extreme Measures
Doctor Bashir and Chief O'Brien trick Section 31 operative Luther Sloan into coming to DS9, then attempt to retrieve the cure for Odo's disease from him.
- The Dogs of War
Kira and the Cardassians are ambushed on Cardassia. Quark is named as the new leader of the Ferengi Alliance.
- What You Leave Behind
The Dominion war comes to a close with the final assault on Cardassia.