The Federation and the Klingon Empire are now at war, and the only way to stop it is to prove that Gowron, the leader of the Klingon High Council, is a changeling. To expose the spy, Sisko and three officers - Worf, O'Brien, and a now-human Odo - must infiltrate a Klingon ceremony in disguise, and activate devices which will cause the changeling to lose its shape. But getting there, and staying undetected long enough to accomplish their mission, is much easier said than done.
Sisko is leading an away team conducting a mineral survey on a planet in the Gamma Quadrant, when a Jem'Hadar warship crashes nearby. The team investigates and decides to take it home as a potentially invaluable aid to Starfleet intelligence. However, another Jem'Hadar ship arrives and destroys the away team's runabout. It soon becomes plain that the Jem'Hadar and their Vorta supervisor desperately want something aboard the crashed ship. To stay alive, Sisko and the others must find out what it is.
Grilka, Quark's Klingon ex-wife, returns to the station seeking Quark's help with getting her troubled house back on its feet. When Worf sees her, he is instantly smitten with a case of par'mach - the Klingon word for love, with more aggressive overtones. However, he finds himself coaching Quark in Klingon courting rituals, language, and fighting, with the help of Dax...who has a few designs of her own. Meanwhile, Kira and O'Brien become uncomfortably aware of their proximity.
Jake has accompanied Bashir to a medical conference, to do a profile on the doctor for a magazine. They are returning to the station when they receive a distress call from a colony under Klingon attack. While Bashir joins the medics in saving and caring for the wounded, Jake has his first up-close experience with the horrors of war. Under the pressure, he does the unthinkable - he breaks down and runs, just when he is needed most. Afterwards Jake must face his guilt and shame, and learn where the fine line between courage and cowardice is.
O'Brien welcomes his wife Keiko back from her visit to the Fire Caves on Bajor, only to learn that she has been taken over by a being who threatens to kill her body unless O'Brien completes certain reconfigurations to the station's systems. With no way to disable her or warn his fellow officers, O'Brien must stay silent as he works on his task - a task which will result in the deaths of the Prophets inside the wormhole.
The Defiant is transporting an Orb which the Cardassians are returning to Bajor - the Orb of Time. Also present is a human merchant who was trapped on Cardassia by the Klingon invasion. The merchant is actually Arne Darvin, a disgraced Klingon spy whose downfall came 105 years ago at the hands of James T. Kirk. Darvin uses the Orb to transport the Defiant back to that time period. The DS9 officers must infiltrate the Enterprise and space station K7 to stop Darvin from assassinating Kirk, and at the same time must prevent the timeline from being altered.
Dax and Worf are going to Risa for a vacation and to work out some kinks in their relationship. They are accompanied by Leeta and Bashir, who are going in order to enact the Bajoran Rite of Separation, and by Quark, who is eager for some 'jamaharon' Worf, displeased with Dax's refusal to take their relationship as seriously as he would like, and disapproving of the pleasure-seeking Risian lifestyle, is attracted by the words of Fullerton, leader of a movement seeking to restore traditional Federation morals and culture, who plans to shut down Risa by any means necessary.
Odo, Sisko, Dax, and Garak are returning in a runabout from a conference on the occupation. When the runabout arrives back at the station, however, they are found in a catatonic state with their minds active, seemingly the result of a plasma storm. Meanwhile, the four find themselves living the roles of Bajorans on Terok Nor during the occupation. Strangely, the security chief is Odo's predecessor, Thrax, although all signs point to it being the time period after Odo had become chief. And, according to Odo, the Bajorans they are supposed to be are soon to be unjustly executed for attempting to kill Gul Dukat.
Odo is escorting Quark to a hearing of the Federation Grand Jury, when Quark finds a bomb on the runabout. Odo is able to channel most of the explosion into the transporter buffer, but it still causes the runabout to crash-land on a mountainous, cold planet. With the subspace booster damaged, they have to get the transmitter up high enough to send a signal off planet...if they don't kill each other first. Also, Nog returns to DS9 as a second-year cadet for field study, and moves in with Jake, only to find that it's not as easy to live together as they had thought.
After seeing a painting of B'Hala, Sisko becomes inspired to seek the legendary lost Bajoran city, guided by markings on an obelisk that mark the city's location by the position of the stars. Sisko replicates the obelisk in a holosuite to try and recreate the missing markings, but the computer shorts out and knocks him unconscious. Due to this experience, Sisko has visions that may reveal the fate of Bajor - but the price may be his life.
A Vedek is killed during a religious ceremony - Latha, a member of Kira's former resistance cell. Kira gets a message with an electronically scrambled voice saying 'That's one.' Someone has a vendetta against the Shakaar, and kills four more of Kira's friends, each time sending another message of the same sort. It is clear that the murders are all connected to Kira, and that she is the killer's ultimate target. Kira, who is still heavily pregnant, defies advice to go off on a personal mission to find the person who is killing her friends.
When Quark sells him an injured baby Changeling he obtained through a trader, Odo becomes determined to find a way to communicate with it by teaching it to shapeshift. Unwanted help arrives in the form of Dr. Mora, the Bajoran scientist who studied Odo. Mora advocates the electrostatic techniques he used with Odo, while Odo is determined not to subject the Changeling to the pain he went through in his early days, their arguments resurrect the bitterness of their past history. Meanwhile, Kira prepares to give birth to the O'Briens' baby at last.
Eight months after Lt. Commander Michael Eddington betrayed Sisko and deserted Starfleet to join his fellow Maquis confederates, he resurfaces, and as the Defiant follows, Eddington triggers a cascade virus that renders the Defiant's computer useless. An angry Sisko is forced to let another captain take over the search for Eddington, as Eddington begins unleashing biogenic weapons against Cardassian colonists in the DMZ. When Sisko decides to go after Eddington regardless, he must face the possibility that he is becoming dangerously obsessed.
A coded message comes through the wormhole from the Gamma Quadrant, which Garak recognizes as a signal from his old superior and mentor, Enabran Tain, who had been presumed dead in the Dominion massacre of the Obsidian Order/Tal Shiar fleet. Worf and Garak are sent to investigate, but they are captured by Jem'Hadar and put in a prison where they find Tain, the real General Martok...and someone familiar from DS9 who has been replaced by a Changeling. Meanwhile, Sisko is faced with an imminent Dominion invasion, and must make the decision to close the wormhole.
As a Dominion fleet comes through the wormhole, Dukat joins them, announcing that after months of secret negotiation, Cardassia is now a member of the Dominion. Dukat is now head of the Cardassian government. The Klingons are expelled from Cardassian space, and Dukat vows to retake the station, a new era dawns when Sisko meets with Gowron. Meanwhile, Garak and Bashir work on an escape plan, while Worf is put to work helping the Jem'Hadar train by fighting them. And the search for the saboteur aboard DS9 goes on.
Dr. Louis Zimmerman arrives on DS9 to work on a Long-term Medical Hologram, the template of which will be based on Dr. Bashir. He begins interviewing Bashir's friends and colleagues to create a psychological profile. To Rom's dismay, Zimmerman pursues Leeta, the object of Rom's secret affection. To Bashir's consternation, Zimmerman invites his parents to the station against his wishes, a development which threatens to bring Julian's darkest secret to light.
Shortly after Odo meets Arissa, a woman visiting the station, she is caught breaking into the computers. She was trying to find a man she was planning to meet - a man who had information on the whereabouts of her long-lost daughter. Odo soon learns the truth - Arissa is trying to leave the crime syndicate she has been working for, and which has sent hit men to kill her and obtain a data crystal containing vital information. With Arissa under his protective custody, Odo discovers something unexpected happening...he is falling in love with her.
Ever since being blackballed by the FCA, Quark has been up to his lobes in debt. Having put his bar up as collateral, he faces losing everything when his investments fail. To the rescue comes his cousin Gaila, who wants Quark to eventually take his place in the arms dealing business, and introduces Quark to his dangerous associate Hagath. Though the Bajoran government refuses to touch their dealings, Quark finds himself ostracized by the station's Federation citizens. And he also finds himself in a moral dilemma when Hagath makes a deal that will cause the deaths of 28 million people.
Kira is delighted by a visit from former Legate Tekeny Ghemor, the Cardassian who once mistakenly believed her to be his daughter, until she learns he is dying. In keeping with Cardassian tradition, he wants to pass on his secrets to be used against his enemies, secrets that could prove damaging to the new Cardassian/Dominion alliance - and which Gul Dukat hopes to prevent from coming to light, as Kira struggles against memories of the death of her own father.
Depressed over his lot in life--especially being blacklisted by the Ferengi Commerce Authority--Quark goes to his homeworld of Ferenginar for some comfort from his mother, Ishka. The free-thinking Ishka is sympathetic, but clearly uneasy over his declaration that he will be 'living' with her for an unspecified period of time. Quark soon learns the reason behind her uncertainty. When he enters his old bedroom, he finds Grand Nagus Zek--the Ferengi leader--hiding in the closet! It turns out that Ishka and Zek are in love. When Quark discovers an underhanded way to get a new business license, will he sacrifice his mother's happiness in order to regain his standing in Ferengi society?
Martok is ordered by the Klingon High Council to command the Bird of Prey Rotarran to search for the battlecruiser B'Moth, which has gone missing while on patrol of the Cardassian border. Martok takes Worf along as his first officer, as well as Dax as science officer. But trouble begins brewing on board when it seems Martok, who spent two years as a prisoner of the Jem'Hadar, would rather avoid Dominion patrols than fight - and Worf must challenge Martok for command.
The Defiant encounters a planet surrounded by an energy barrier, in the Gamma Quadrant. Dax is eager to check it out, but as they penetrate the barrier, Kira is hit by a discharge. The crew is greeted by the inhabitants, who are their descendants, the result of an anomaly which caused the Defiant to crash on the planet, 200 years back in time. Kira - who learns of Odo's love for her from an older version of him - is destined to die unless she gets back to DS9. The crew must choose whether to let themselves be stranded and allow Kira to die, or to wipe out the existence of the colony.
Despite the fact that the Maquis have been decimated by the Cardassian/Dominion alliance, a message to Eddington is intercepted, saying that cloaked missiles have been launched toward Cardassia. Hoping to prevent a retaliatory war, Sisko appeals to the imprisoned Eddington to help deactivate the missiles before they reach their target. Promised freedom, Eddington agrees - but warns Sisko that he intends to kill him once the mission is over.
O'Brien leads a salvage team to Empok Nor, an abandoned Cardassian space station in the Treba system, to obtain needed spare parts for DS9. The team includes Nog as well as Garak, whose help is needed in disarming the booby traps the Cardassians left behind. However, the team soon finds themselves stranded on the station and stalked by three Cardassian soldiers - test subjects for an experimental drug to heighten their racial xenophobia - and Garak too has now been exposed to it.
An air of depression hangs over Deep Space Nine, as rumors of impending war with the Dominion fly, and Kai Winn visits the station to meet with the Vorta, Weyoun, regarding a possible non-aggression pact. Seeing his father's dejected mood, Jake resolves to do something for him to cheer him up. With Nog's help, he bids on an antique baseball card at an auction, but is outbid by Dr. Giger, an eccentric scientist. Jake is still determined to get the card. After all, how hard can it be?
In order to stop the Dominion from sending caravans to Cardassia, Starfleet authorizes Sisko to place a minefield at the entrance to the wormhole. With war now imminent, a Bajor/Dominion non-aggression pact is signed with Sisko's endorsement, to ensure Bajor's survival. Rom and Leeta are married, and Worf and Dax become engaged, while Odo and Kira agree to set aside their relationship for now. When the Dominion attacks, the station must fight them off until the Defiant finishes setting the minefield - but all may already be lost.