With Deep Space Nine under the control of the Dominion, the situation around the wormhole is out of the Federation's hands. Their only trump card is the mine field, which will continue to create new mines as others are detonated when any ship attempts to enter or exit the wormhole in the Alpha Quadrant. Three months later, the new residents of DS9 are having trouble disabling the mines. Fortunately for them, the three-month-long Dominion War finds them in a better position as Federation forces continue to lose ground to the new force in the Quadrant.

On Deep Space Nine, Odo made a request to the Vorta, Weyoun, that his Bajoran security team be reinstated. Taking the request as an order from a god, Weyoun readily agrees provided that Odo join the station's council that includes Weyoun and Gul Dukat. Meanwhile, Captain Sisko and his team have destroyed a Dominion supply station of Ketracel-White, the only way that the Jem'Hadar can survive. Unfortunately, they were caught in the blast and their Jem'Hadar ship is severely damaged. With warp drive out, the former ops crew of Deep Space Nine is as good as stranded.

While Major Kira and Odo plan the resistance, Gul Dukat returns from Bajor with Ziyal, who has a very important announcement for the Major and Dukat to hear. Onboard the Klingon vessel IKS Rotarran, Worf and General Martok receive their orders to escort a convoy on a perilous, and glorious, mission that could mean certain passing. One of the new enlistees to join the Rotarran is Alexander Rozhenko, Worf's son.

Stardate 51145.3: With the assistance of Rom, Major Kira's plan to turn the Cardassians and the Jem'Hadar against each other enters the first stage. Light years away, on Starbase 375, Captain Sisko is told of a communications array being used by the Dominion to track Federation movements. Located in a star cluster, the array is heavily defended, making a plan of attack difficult. There may only be one way to destroy the array and it's a risky course of action.

With Odo no longer on the Major's side and the minefield about to be destroyed by Deep Space Nine's deflector array turned anti-graviton field, things look bad for the resistance on the station. The Federation's morale continues to drop. With each successful engagement, an inevitable retreat soon follows. However, Captain Sisko has a plan to turn the tide: Retake Deep Space Nine.

The Federation advances on Deep Space Nine with nearly the entire Dominion's Alpha Quadrant fleet waiting for them. Outnumbering Starfleet two to one, the only edge that Captain Sisko has is to create a hole in the wall of Dominion and Cardassian vessels and race towards DS9. On the station, the situation looks grim as the Major and her collaborators are to be arrested for crimes they did not commit. Fortunately, the former crew of Deep Space Nine is full of surprises.

Stardate 51247.5: Due to Alexander's new assignment aboard another Klingon vessel that will take him far from Deep Space Nine, Dax pressures Worf into pushing up the wedding date and holding it at the station. While Worf and Martok leads the men in the Klingon groom's ceremony, Dax is given the test of the House of Martok by Martok's wife, who will see if Dax is fit to join the family.

Dax tries to set the Major up for a dinner date, but Kira is not interested in bringing anyone. Even the company of Odo would, at present, not be realistic. The conversation is put aside when a man beams into Ops from an unknown location. When he reveals himself to Kira, the Major recognizes him as Bareil from the alternate universe.

Doctor Bashir meets with a group of people who, like him, had their DNA altered to make them better. Unfortunately for these people, they suffered serious side-effects of the treatment and developed psychological illnesses that are difficult to reverse. Doctor Bashir attempts to find a solution to the problem.

Jealous of the Starfleet soldiers onboard Deep Space Nine using their hero stories to trump his stories of profit, Quark suddenly finds himself in a position to become a hero himself. His mother has been kidnapped by the Dominion and Grand Nagus Zek is paying Quark to rescue his mother. Quark puts together a team of seven Ferengi in order to save the day.

While accompanying Gul Dukat to his first hearing on his war crimes, Captain Sisko and the rest of the USS Honsh? are attacked by the Dominion. When Sisko awakens, he is on a planet with his left arm in a cast and Gul Dukat as his only companion. Dukat was able to save Sisko by making it to a shuttle with the Captain in tow. On the surface of a barren planet, their now repaired distress beacon will hopefully send help.

Word comes in to Deep Space Nine that Morn, the resident barfly of Quark's, has passed on. A lavish wake is held in his honor and all of DS9 mourns his passing. Quark feels the worst because he figures that without Morn he will lose business. However, once he is told by Odo that he is the benificiary of Morn's estate, he quickly forgets his troubles.

The loss of another friend in the Dominion War is slowly sapping Captain Sisko of his energy and he is becoming frayed around the edges. With his father visiting the station, Sisko begins to question his place in the war. Then, the synaptic problems that almost caused his passing ("Rapture") resurface and he is thrown back in time to Earth in the mid-1950s, to experience the fifties from the point of view of an SF pulp magazine writer, as well as the life of a black man in a still racially segregated culture.

Stardate 51474.2: A science expedition goes awry when a Jem'Hadar ship attacks the Defiant. Before the attack, the Runabout Rubicon had entered an anomaly that rendered it only a foot across. Lieutenant Commander Dax, Doctor Bashir, and Chief O'Brien were the three in the Rubicon when it entered the anomaly. Now, in their minuscule form, they must find a way to communicate with the Defiant.

Deep Space Nine is suffering from numerous glitches. The station's two systems, Federation and Cardassian, are not working well together and the only man who can fix the problems is Chief O'Brien, who is away on assignment. The Chief has gone undercover for Starfleet Intelligence in order to find a Starfleet mole working for the Orion Syndicate. He is able to infiltrate the group with his engineering skills. Now comes the hard part: Being accepted by the Syndicate.

Stardate 51597.2: Worf and Jadzia have been ordered to the Badlands to receive an encrypted transmission from a Cardassian spy who has requested that Starfleet Intelligence be prepared to receive a very urgent message. On their way to the rendezvous point, they plan their honeymoon.

Major Kira purchases some Bajoran lilacs to honor her mother's birthday. She didn't know much about her mother other than what her father told about her. Unfortunately, just before her mother's birthday, Gul Dukat calls and tells the Major that her mother was once his. Determined to prove him wrong, Kira looks into the Cardassian Occupation records.

Doctor Bashir gears himself up for a medical conference on Casperia Prime, one of the vacation planets. Unfortunately, his trip is cut short before it even starts. Starfleet Intelligence has reason to believe that their is a spy aboard Deep Space Nine and all evidence suggests that it's a member of the senior staff. Interviews are conducted by Internal Affairs in order to find out if their is a spy or not.

Stardate 51721.3: Captain Sisko records a personal log in which he lays out the mistakes he made in his attempt to change the course of the war with the Dominion. Two weeks ago, in order to put the all the powers into position, he decides that the Romulan nonaggression treaty with the Dominion will have to be annulled so that the Romulans will join the Federation and push the Domonion out of the Alpha Quadrant once and for all.

Even though Odo's feelings for Major Kira have not diminished, he has been unable to stir up enough confidence to set up a date with her. When the Major returns to Bajor to see First Minister Shakaar, whom she had not seen in over a year, Odo feels that he needs some pointers on romance. He receives an education from a new holosuite program entity that is modeled after a singer from Las Vegas circa 1960.

At the request of the archaeologists excavating B'Hala, Captain Sisko, Major Kira, and Jake journey to Bajor to look at an ancient artifact. The artifact in question is one that carries the inscription "Welcome Emissary" on it. When Sisko touches it, he has a vision of the Prophets in which they tell him that a reckoning must take place.

Stardate 51825.4: Aboard the Runabout Shenandoah, Nog and Jake head to Ferenginar to deliver a diplomatic message to the Grand Nagus. Leaving from Starbase 257, they are attacked by a Jem'Hadar fleet on their way to the base. While the rest move on, one Jem'Hadar ship continues to attack the Shenandoah. Fortunately for the Nog and Jake, they are backed up by a sister ship of the Defiant, the Valiant, which is staffed by members of Starfleet Academy's Red Squadron.

Having trouble reaching anyone on Ferenginar, Rom goes to Quark and begs him to help find out what is going on. Trying to figure out what to do, a Ferengi ship appears with Grand Nagus Zek and Quark and Rom's mother on board. Landing, they tell the two brothers that Zek amended the Ferengi Bill of Opportunities to allow Ferengi women to wear clothes. The result of the amendment led to worldwide panic in the Ferengi stock market that overloaded all of the communications lines. As a result, Zek was deposed and Brunt is now the Grand Nagus. That is, unless Zek can retake his crown.

Excited about a trip to Golana, one of Bajor's neighbor planets, Molly O'Brien goes with her father, mother, and brother to have a picnic. While there, Molly ventures off and falls into a timescape that transports her three hundred years into the past, to a time when there was no civilized life on the planet.

Odo begins to give Quark a hard time about Deep Space Nine's rules and regulations, making running his establishment difficult. That is, until Quark sees that Odo's love for Major Kira has created the perfect way to distract Odo and earn profit. Meanwhile, returning from a convoy mission, a very tired Defiant crew answers a distress call from a Starfleet Captain whose ship crashed on an inhospitable planet. With the clock ticking to rescue her, the Defiant is pushed to its limits while the crew keeps the stranded captain company.

Another Bajoran Gratitude Festival has arrived and, despite the Dominion War, Deep Space Nine celebrates the occasion. Things are not all joyous, however, as Odo has arrested a Vedek for a trivial criminal offense that Major Kira has trouble understanding and a rift has arisen between them. Meanwhile, while receiving another award for meritorious service, Captain Sisko is informed that the Federation, along with the Romulans, will commence an invasion of Cardassia with the Captain as the leader of the offensive.