Stardate: Unknown. Word that a previously thought dead Bajoran resistance legend is still alive sends Kira and Chief O'Brien to Cardassia IV to rescue him; meanwhile "The Circle", a sect of the Bajoran provisional government that is intent on wiping out alien influence, is sneaking into power.
The Circle attempts to topple the Bajoran government, but there is more to the situation than meets the eye. (Part 2 of 3)
Sisko and Li Nalas help stop Deep Space Nine from being commandeered by The Circle, while Kira and Dax try to put an end to the Circle by presenting evidence that Minister Jaro is being backed by the Cardassians. (Part 3 of 3)
Stardate: 47182.1. A jealous Trill, who had waited his entire life to receive a symbiont but never had, decides to steal one. . . Dax's!
Garak investigates the identity of a Cardassian boy, Rugal, abandoned on Bajor, who has been raised by a Bajoran.
Stardate: 47229.1. A new arrival to the station with a special gravity-based disability appeals to Bashir's heart; meanwhile an old associate of Quark's comes to the station to kill the barkeep.
Quark represents Grand Nagus Zek in a plot to establish a Ferengi business presence in the Gamma Quadrant. Pel, a young Ferengi, teams up with Quark and they learn that to do business in the Gamma Quadrant they must contact the Keremma, a member race of the Dominion.
Stardate: 47282.5. Odo relives some terrible and tragic memories of a past investigation when he was the constable on Cardassian-occupied Deep Space Nine, then named Terok Nor.
A mysterious woman, Fenna, catches Sisko's eye during their fleeting meetings. Meanwhile, an extremely egotistical scientist is working on a project to re-ignite a dead star.
Stardate: 47391.2. A race that has been conquered twice over, one of the conquerors being the mysterious Dominion, comes to the station seeking aid and a new home.
Stardate: Unknown. Quark meets his match when a new rival opens a casino opposite Quark's Bar on the Promenade; meanwhile the station is suffering issues of high improbability.
A scientist, Dr. Mora Pol of the Bajoran Science Institute, finds a life-form in the Gamma Quadrant that may be related to Odo.
O'Brien and Bashir help two warring races, the Kellerun and T'lani, erase all knowledge of a deadly biological weapon, but are not trusted to keep what they have learned a secret.
While preparing the station for upcoming peace talks, O'Brien discovers that the crew have been hiding information from him and giving orders behind his back. O'Brien begins to suspect everyone on the station is gradually being altered or replaced by an unknown force.
Commander Sisko and Chief O'Brien are stranded on a planet, Aurelius, where their leader, Alixus, rejects technology, even when it means the death of others.
Stardate: 47603.3. Odo and Dax investigate the mysterious disappearance of people from a village. Kira tries to keep a close eye on Quark, while Vedek Bareil unexpectedly visits.
Dax is supervising Arjin, a Trill candidate for joining, and she helps him find his voice and discover what he wants from life and from joining. Meanwhile, a proto-universe threatens to destroy the station and Bajor.
Quark is reunited with his former Cardassian lover, Natima Lang, but she is engaged in dangerous political intrigue with her students Rekela and Hogue: they want to reduce the political power of the Cardassian military.
Jadzia Dax honors an oath made by Curzon Dax to three Klingons (Kor, Koloth, and Kang), and goes with them on a crusade against their sworn enemy "the Albino" who murdered their firstborn children as revenge for stopping his raid on a Klingon colony.
Stardate: Unknown. The destruction of a Cardassian ship leads Sisko, Dukat, and Sisko's old friend Cal Hudson to the fact that there is an unofficial war between the Maquis and the Cardassians.
Federation colonists reject a treaty with Cardassia and take matters into their own hands by planning to destroy a weapons depot at the Cardassian Bryma colony.
Stardate: Unknown. Dr. Bashir fights to save Garak's life when a malfunctioning Cardassian brain implant threatens to kill him.
Kira and Bashir accidentally cross into the Mirror Universe, where a Klingon-Cardassian alliance rules and Terrans are slaves on the station. A century before, James T. Kirk had made a similar crossover, affecting human and galactic history.
A Bajoran secretary named Kubus, who aided the Cardassian occupation forces, wants to return home from exile. Vedek Winn engages in a power play against Vedek Bareil to become Kai.
O'Brien is declared guilty of an unspecified crime and later "tried" at a tribunal held on Cardassia Prime.
Sisko, Jake, Nog, and Quark go camping on a Gamma Quadrant world. Sisko and Quark are captured by mysterious soldiers called the Jem'Hadar and meet a force, the Dominion, who rival the Federation.