Sisko takes the new USS Defiant into the Gamma Quadrant to find the mysterious leaders of the Dominion and avert a war, while Odo is drawn by instinct towards his home planet in the Omarion Nebula.
Stardate: 48213.1. Odo has found his home and is introduced. Meanwhile Sisko finds out peace talks between the Dominion and the Federation have already started.
Stardate: Unknown. Quark tries to boost his reputation by taking credit for the accidental death of a Klingon in his bar, but lands himself in the middle of a Klingon political struggle.
Stardate: Unknown. 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.
Kira is kidnapped by Cardassians, surgically altered to look Cardassian and told she is actually an undercover Cardassian agent.
Quark purchases a salvaged ship from the Gamma Quadrant and discovers an infant on board. Sisko invites Mardah, the dabo woman Jake is interested in, to dinner. Odo officially gets quarters aboard DS9.
Deep Space Nine is progressively locked down after O'Brien, Jake and Sisko accidentally activate an automated Cardassian security program. The program's counter-insurgency measures keep escalating until it initiates an auto-destruct. Gul Dukat beams on board, but is unable to stop the self-destruct sequence.
Dax falls in love with Deral, who will soon disappear because he is a member of Meridian, a planet that phases between dimensions every 60 years.
Commander William Riker shows up unannounced and Kira shows him the Defiant, where his real identity and his true motives for coming to Deep Space Nine are revealed.
Lwaxana Troi pursues Odo during the Bajoran Gratitude Festival as members of the crew suddenly become infatuated with one another.
A transporter accident sends Sisko, Bashir, and Dax three centuries into Earth's dark past to a time just before the 2024 Bell riots, a violent civil disturbance in opposition to Sanctuaries which are controlled ghettos for the dispossessed.
Sisko assumes the role of a pivotal historical figure, Gabriel Bell, in order to restore the timeline.
Stardate: 48498.4. 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.
When Kira's life is put in jeopardy, Odo expresses the depth of his feelings for her. Meanwhile, back on the station, Nog requests a letter of recommendation to Starfleet.
Despite Trakor's Bajoran prophecy of destruction, Sisko assists in a joint scientific venture with the Cardassians to open communications through the Bajoran wormhole. Sisko is forced to face his status as Emissary seriously in the face of the prophecy.
Quark discovers that Grand Nagus Zek has written a new virtuous and benevolent set of the Rules of Acquisition, which would put an end to traditional Ferengi ways. Bashir is oddly disturbed when he is nominated for a highly prestigious medical award.
Exposure to radiation causes O'Brien to jump five hours into the future for brief periods, including one that shows Deep Space Nines destruction, while the station hosts Romulan and Klingon delegations.
Approaching his 30th birthday, Julian Bashir is subjected to a telepathic attack by an alien seeking a restricted substance. He wakes up to find the station almost deserted and that he is aging rapidly.
Stardate: Unknown. Sisko is kidnapped to impersonate his deceased, mirror universe self to gain Jennifer Sisko's loyalty in the Rebel Alliance.
Garak's tailor shop is bombed, forcing Odo to investigate who is trying to kill the Cardassian exile – and why. (Part 1 of 2)
Garak reluctantly tortures Odo for information to prove his loyalty to his former mentor, Enabran Tain, as a joint Tal Shiar/Obsidian Order attack on the Founders in the Omarian Nebula is underway. (Part 2 of 2)
Sisko builds a replica of an ancient Bajoran space vessel and with Jake attempts to prove that the Bajorans developed interstellar travel before Cardassians. Bashir frets over the impending visit of the classmate who graduated first in his class at Starfleet Medical Academy.
Quark returns to his home planet to confront his mother (Moogie) after hearing from the Ferengi Commerce Authority that she broke the law by earning profit. Sisko meets Captain Kasidy Yates as a romantic interest, which Sisko has discovered his son has told most of the station about.
Kai Winn needs Kira to convince the former resistance leader Shakaar, now a farmer on Bajor, to return soil reclamators needed elsewhere in Rakantha, which used to be Bajor's most productive agricultural region.
Jadzia Dax deals with feelings of inferiority as she encounters past hosts in a Trill Zhian'tara ceremony, which is able to transfer the memories of former hosts into another recipient, and Odo takes on the role of Curzon Dax during the experience.
Ambassador Krajensky informs newly promoted Captain Sisko that there has been a coup on Tzenketh. He orders Sisko to take the Defiant to the nearby Federation colonies to ”show the flag” and keep the Tzenkethi quiet. Meanwhile, a Changeling hides on board the Defiant and sabotages the ship.