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.
Sisko becomes uncomfortable when the Klingons station a task force to help defend against the Dominion. Worf is summoned to find out their true intentions.
Melanie, an aspiring writer, wants to know why Jake Sisko stopped writing at 40. Jake tells how his father died in an accident and then suddenly reappeared.
Bashir is asked to help a group of renegade Jem'Hadar break their addiction to ketracel white. Meanwhile Worf is dissatisfied with the way Odo runs security.
Kira and Gul Dukat go after the lost prison ship Ravinok. Dukat has a secret. Meanwhile Kasidy Yates tries to find work near Bajor, leaving Sisko uncomfortable.
Lenara Kahn, the new host of the wife of Dax's former host Torias, comes to the station. While they're not allowed to renew their relation, there's still a spark.