Tahna Los, a former Bajoran terrorist during the Occupation, asks Sisko for asylum on DS9. Meanwhile, the station's last Cardassian inhabitant, Garak, possibly a former spy for the Cardassian government, proves an interesting mystery to Dr. Bashir.
Ibudan, a criminal Odo has dealt with before, returns to DS9 only to be murdered shortly after - leaving Odo to be the prime suspect. Jake and Nog's trouble making prompt Keiko to do something helpful for the station's children.
The crew and civilian population of Deep Space Nine begin to speak gibberish when a plague - an 'aphasia virus' - engineered by the Bajorans as a weapon against the Cardassians, accidentally gets released into the station's atmosphere.
The entire station's command staff, save Odo, become power hungry and vie to defeat each other by forming secret alliances and plotting assassinations. Odo tries to figure out the cause of this mysterious behavior.
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.
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.
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.
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.
Dukat returns, stripped of his prestige, to escort Kira to a Cardassian conference about the Dominion. But an attack by a Klingon raider may give Dukat a chance to redeem himself in the eyes of his government.
A mysterious woman approaches Jake about his future as a writer. Odo promises to do whatever it takes to help Lwaxana Troi keep her baby over the father's wishes - even if it means marrying her himself.
The discovery of an infant Changeling gives Odo a chance to correct what he sees as the "mistakes" in his upbringing. But as Starfleet's pressure for results grows, he has to turn to his "father," Dr. Mora
A coded message from the Gamma Quadrant leads Garak to believe his mentor, Enabran Tain, is still alive. He and Worf seek him out, only to discover something much worse: a Dominion invasion fleet poised to attack the Alpha Quadrant.
Dr. Bashir is selected to be the model for the next-generation of Emergency Medical Hologram (EMH). But he balks when his parents are invited to the station to be interviewed by the EMH programmer, Dr. Zimmerman. There is a dark secret in his family that he's afraid that his parents will reveal.
When a Cardassian official ([link=nm0696303]), who thinks of Kira ([link=nm0000684]) as his daughter, is dying, he agrees to reveal all he knows to her. But the experience dredges up Kira's memories of her own father's ([link=nm0465664]) death.
The DS9 crew discovers a small colony on a remote world that was originally populated by them 200 years earlier due to a time-travel accident with the Defiant. The current colonists lives depend on making sure that accident happens again, even though they've now forwarned the crew that it will happen. Each crew member needs to decide if they are willing to give up their lives on DS9 in order to preserve the history of the colony.
Jake and Nog go through hell and high water, from participating in an auction to dealing with the Dominion, to receiving a Willie Mays baseball card, all in order to cheer up the war-fatigued Captain Sisko.
With the continuing battalions of Jem'Hadar entering the Alpha Quadrant in preparation for war, Sisko decides to mine the wormhole to prevent further troop movement. This provokes a confrontation between the Dominion and the Federation, forcing Sisko to abandon DS9.
Sisko and his crew crash on a barren world when their commandeered Jem'Hadar ship is shot down. They encounter Jem'Hadar who crashed there earlier, and have taken Nog and Garak hostage in exchange for medical aid for their Vorta overseer.
After forming an attack plan on the Dominion, Sisko relinquishes command of the Defiant to Dax after accepting a promotion. On DS9, the resistance faces discovery when Odo links with another changeling.
Suddenly desiring to wed within the week on DS9, Worf and Jadzia go through their own Klingon rituals: Worf on a four day bachelor party with the male members of the crew & Jadzia deals with her prospective mother-in-law, who totally opposes the idea of "an alien" marrying into her Klingon household.
A Dominion attack on the Defiant endangers Dax, Bashir and O'Brien aboard the runabout U.S.S. Rubicon as they enter an anomaly that shrinks them to a very minute size. Unfortunately, they were being held stable by the Defiant within a tractor beam, which was discontinued during the attack.
Worf and Jadzia travel to the badlands to procure some information on the Dominion from a traitorous Cardassian. Bashir wants to engage in a holo-suite spy simulation, but O'Brien prefers to brush up on his tongo game after watching Jadzia lose to Quark.
Spiritualists on Bajor summon Captain Sisko to the planet surface, where they show him a stone tablet with some unknown inscriptions. Once on DS9, the inscription reveals an ancient prophecy of coming disasters surrounding the wormhole, Bajor, and DS9, as those around him voice their uneasiness about Sisko being an Emissary for the planet.
Quark's mother and the Grand Nagus show up on DS9, announcing a new amendment to the Bill of Opportunities he has instituted on the home planet of Ferenganar, and then follows up with the announcement, that, due to the new amendment, chaos has followed and he has been deposed.
Having returned to Earth a couple of months ago, Sisko waits for the Prophets to instruct him on what to do next. When he receives one, he begins searching for the woman behind the face in the sand in his vision. Meanwhile, back on DS9, Kira deals with a promotion and handling the decisions surrounding her command, and finding herself wishing for the return of Sisko. And Worf deals with the loss of his wife, Jadzia Dax.
Ezri Dax joins Sisko and his family on his quest for the Orb of the Emissary. Colonel Kira mounts a blockade around a Bajoran moon, where the Romulan hospital is - along with thousands of Romulan missles (claimed to be defensive in purpose). Quark joins Bashir & O'Brien as they join Worf, aboard a Klingon warship as they mount a dangerous mission in Jadzia Dax's name in an effort to get her spirit into Sto-vo-kor, the Klingon's heaven.
Sisko tries to convince Ezri to stay in Starfleet and serve aboard DS9, as Ezri tries to get to know Jadzia's friends aboard the station, especially Worf. Meanwhile, Garak tries to deal with a severe bout of claustrophobia.
When a programming glitch won't go away, mobsters take over Vic's and open for business, but the DS9 gang takes it personal when their favorite hangout is no longer their favorite, and they plan to get the new management ousted.
While making plans to attend a medical conference on the Romulan home world, Dr. Bashir is contacted by Sloane of Section 31 and recruited to determine the health of a high-ranking Romulan official. Things turn more desperate, though, when the ranking Starfleet admiral traveling with him, who knows about Section 31's interest in the conference mysteriously suffers a brain aneurysm after Dr. Bashir finds out that Sloane is traveling with the group, as well.
The Prophets have told Sisko they do not approve of his impending marriage. Having been captured by the Breen, Ezri and Worf still don't know why the Breen would even bother to capture them. Some Cardassians are beginning to think their alliance with the Dominion was a grave mistake. Gul Dukat, disguised as a Bajoran, sets foot on DS9, and continues to unfurl his plan.
Kai Winn gets unknowingly involved with Gul Dukat, surgically altered to resemble a Bajoran, using the name 'Anjohl.' Tensions further escalate between Weyoun and Legate Damar, as the Dominion gather to sign a peace treaty with the Breen, which includes granting the Breen certain Cardassian territories. Having been held captive by the Dominion, Ezri and Worf try to escape from the Cardassian home world.
After the Breen attack Earth, mixed emotions abound on DS9. Kai Winn reveals her true feelings regarding the Prophets to her spiritual guide, a Bajoran farmer named Anjohl, who is a surgically altered Dukat, and turns her back on them, and convinced by him to embrace the Pah Wraiths. On the home world of Cardassia, Legate Damar mounts a resistance to the Dominion.
Kira gets sent behind Cardassian lines in an effort to train them in resistance fighting. When Dr. Bashir learns of the deadly disease Odo is infected with, he gets met with resistamce whilst trying to obtain his medical records from Starfleet. Martok gets blindsided by Gowron when he arrives on DS9, announcing he has assumed command of the Klingon fleet.
Odo is affected by the disease threatening to eliminate his race more than he lets on, while Kira has to deal with the Cardassians' dislike of her. Even though General Martok sees Chancellor Gowron's move as part of a political vendetta, he does nothing about it. Worf suspects Gowron's military strategies are meant to humiliate Martok's command abilities, without thought the consequences have for Klingons as a whole. Meanwhile, O'Brien suggests to Bashir he announce he's found a cure to the Changelings' disease to lure someone from Section 31 to DS9.
Odo begins recovery from the deadly disease which Dr. Bashir tells him had been engineered by Section 31 in order to wipe out the Founders' entire race, A resistance mission goes bad for Kira and Garak, and they end up hiding in the basement of the house which Garak grew up in. They soon hear Legate Damar - who had been on their mission and was hiding with them - has just become a casualty of war. The Grand Nagus has chosen Quark to become his successor, upon his impending retirement on the pleasure planet, Risa.
As the Dominion War comes to an end, Dukat goes to the Pah Wraiths to awaken them. Meanwhile the Dominion turn on the rebelling Cardassians, destroying them city by city. Will the Alliance prevail over the Dominion? Will Garak and the Rebellion stop them before the destruction of Cardassia? Will Sisko stop the Pah Wraiths from rising?