In their second year together, the crew of Deep Space 9 face problems that will affect the galaxy forever. A Bajoran extremist group attempts to force the Federation out of the Bajoran system. The Cardassians are secretly supplying them with weapons, hoping to return to reclaim the planet and hold the Bajoran wormhole for the Cardassian Union. However, the greatest enemy of all is lurking beyond it.
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.
Stardate: Unknown. As a "Circle"-led Bajoran military tries to occupy the station, a skeleton crew led by Sisko fight to reveal "The Circle's" big secret before they are forced to evacuate themselves. Meanwhile, Kira and Dax lead a mission to reveal the truth about "The Circle" on Bajor.
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.
Stardate: Unknown. A female Ferengi, posing as a male to be available to participate in business (a rule STRICTLY forbidden by the Ferengi government), falls for Quark during very important negotiations between the Ferengi and a Gamma Quadrant race.
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.
Stardate: 47329.4. While noted scientist Gideon Seyetik is preparing for an ambitious project, re-igniting a star, Sisko is intrigued by a woman who keeps disappearing.
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.
Stardate: 47529.4. Chief O'Brien, who still doesn't like the good Doctor Bashir, must rely on him when the two are stranded on a planet and O'Brien is infected with a deadly, fast moving disease.
Stardate: 47581.2. Chief O'Brien's world is turned upside down when for no reason whatsoever he is being ignored by his family and friends and is being closed out of every essential job on the station.
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.
Stardate: Unknown. A Trill named Arjin comes to DS9 to learn what it is to be a Trill with a symbiont but finds his teacher, Dax, to be less than he expected.
Stardate: Unknown. Three legendary Klingons come to DS9 to see if Jadzia Dax will participate in a Blood Oath they made with Jadzia's previous host Curzon.
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.
Stardate: Unknown. Sisko tries to resolve the Maquis crisis by preventing a war, freeing Gul Dukat and offering the defected Hudson the chance to return.
Stardate: Unknown. Dr. Bashir fights to save Garak's life when a device implanted in his brain, designed to alleviate pain in the event of torture, begins to malfunction and is slowly killing him.
Stardate: Unknown. Vedek Bareil is targeted by fellow Kai candidate Vedek Winn as having been a collaborator with the Cardassians during the Occupation.