Instead of waiting for the Jem'Hadar to attack, Sisko wants to try a different tactic; he wants to take a new class starship to try to find the Founders.
The Trill homeworld is the setting, as Sisko and Bashir take Jadzia home for treatment when she begins experiencing hallucinations after playing a tune she can't recall.
Odo tries to change the nature of a rapidly maturing Jem'Hadar infant Quark finds, while Sisko tries to break his son's relationship with a 20 year old Dabo girl.
Riker arrives on the station to requisition the Defiant in order to fight with the Maquis. Sisko assists Gul Dukat on Cardassia Prime to prevent the ship from entering Cardassian territory.
Sisko, Bashir and Dax are accidentally sent to San Francisco in the 21st century due to a transporter malfunction, and must figure out how to get back to return without changing the time line.
Dr. Bashir must use extraordinary measures to prolong Vedek Bareil's life long enough to allow Bareil to complete sensitive peace negotiations between the Bajorans and the Cardassians.
After chasing a fugitive into a cave, Kira gets stuck and is slowly encapsulated by a growing crystal stone while Odo tries to figure out how to free her.
Sisko faces a conflict between his Starfleet duties and his role as the Bajoran Emissary when an ancient Bajoran prophecy predicts a joint Federation-Cardassian project will lead to the destruction of the wormhole.
While a Romulan delegation tries to get information about the Dominion, O'Brien gets visions of unpleasant things that are about to happen in the future.
After being attacked in the infirmary, Dr. Bashir has a dual mystery on his hands: what has happened to the station while he was out and why is he aging so rapidly now?
Sisko is kidnapped and forced to impersonate his deceased mirror universe counterpart in order to convince Jennifer Sisko to defect to the Terran Rebellion.
Now rejoined with his former mentor, Garak is ordered to interrogate Odo about the secrets of his people, while the joined Romulan/Cardassian attack fleet moves towards the Founders' home world on a mission of destruction.
Sisko rebuilds an ancient Bajoran space vessel from the blueprints, and he and Jake take the ship on a trip, attempting to prove that the ancient Bajorans went beyond their solar system without warp drive.
Quark and Rom return to the Ferengi home world because their mother has broken the law - by wearing clothes and earning profits, forbidden for women in Ferengi society.
News arrives that Kai Winn has also become Bajor's political leader. She asks Kira to negotiate with an old resistance friend about returning soil reclamators.
The Defiant is off to show the Federation's presence to the new Tzenkethi government. While underway the ship malfunctions and repeated instances leads Sisko to believe a changeling's onboard, engaging in sabotage.