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.
As a Circle-led Bajoran military attempts to occupy the station, a skeleton crew, led by Sisko fight to reveal the Circle's secret before they're forced to evacuate themselves. Meanwhile, Kira and Dax lead a mission to reveal the truth about the Circle, on Bajor.
Melora Pazlar, a new arrival on DS9 with a special gravity-based disability, finds an admirer in Bashir. Meanwhile, an old associate of Quark's comes to the station to kill the bartender.
A female Ferengi named Pel, posing as a male so that she can engage in business, falls for Quark during very important negotiations between the Ferengi and a Gamma Quadrant race.
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.
Quark meets his match when a new rival opens a casino opposite his bar on the Promenade. Meanwhile, the station is suffering issues of high improbability.
Chief O'Brien, who still doesn't particularly like 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.
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.
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.
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.
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.