With the unpleasant introduction of the Dominion to the Federation, the Alpha Quadrant begins to worry about a possible invasion from their neighbors in the Gamma Quadrant. Major Kira has run countless simulations on a possible attack and Deep Space Nine is always shown to be vulnerable. As Ops meets to discuss the matter further, a cloaked ship appears almost within the range of the station's shields. As the crew watches the ship uncloak, they notice that it bears the nomenclature of a Starfleet ship. Commander Benjamin Sisko hails the station from the vessel, introducing his staff to the USS Defiant. Armed with the latest Federation vessel, the crew of Deep Space Nine head into the Gamma Quadrant to find the Dominion's leaders, known only as the Founders.

Lieutenant Dax and Chief O'Brien have been taken prisoner by the Dominion and the Jem'Hadar have rendered the USS Defiant null and void. The only ones to survive the attack between the Defiant and the Dominion were Major Kira and Odo, who was able to escape with the unconscious Major on a shuttlecraft. Drawn by an unknown power, Odo takes the shuttlecraft to the Omarian Nebula. There, Odo and Kira come across an M-Class planet that is the home of the Changlings.

An incredibly slow night at Quarks leaves a drunken Klingon as their only patron. The Klingon asks for a line of credit, which Quark at first refuses, but changes his mind once the Klingon becomes agitated. However, before Quark can say anymore, the Klingon attacks him with a knife. In the ensuing scuffle, the Klingon pierces his own heart with the blade. In the aftermath, business begins to boom at Quark's as rumors spread, from Quark's own tall tale, that he defended himself valiantly against the Klingon warrior. Meanwhile, with the threat of the Dominion ever present, most of Keiko's students have relocated to Bajor so Keiko shut down the school.

While attending a dinner prepared by Commander Sisko, Jadzia Dax finds an electronic piano once played by Jake. While the others enjoy the food, Jadzia continues to try to play a piece that is floating around in mind. Later, she starts to have hallucinations about a mysterious cloaked figure wearing a mask. A check-up reveals that her connection with the symbiont is growing weaker. Commander Sisko and Doctor Bashir return with Jadzia Dax to Trill to find out from the host doctors what is going on.

Major Kira receives a call from the Bajoran Central Archive requesting information on her incarceration at a prison on Bajor during the Cardassian Occupation. However, the Major remembers quite vividly that she was hiding with the Bajoran resistance at the time of her supposed stay in the prison. She travels to Bajor to sort out the mess, but is kidnapped and taken to Cardassia.

Quark is offered what is left of a destroyed ship from an old business associate. What is left of the ship is sold to him for a bargain price of three bars of gold pressed latinum. Upon inspecting the wreckage, Quark discovers a baby in on sealed chamber. Examining the baby reveals an incredible maturation rate. It isn't long before the baby becomes a fully-grown boy.

While working on the uridium ore processing facility in order to turn it into a deuterium processing facility, Jake Sisko and Chief O'Brien come across a file that doesn't have a name and cannot be deleted. Trying to override the file initiates a localized shutdown of the ore processing area, which had been put in place by the Cardassians in case of a Bajoran revolt during the Occupation. The more the Deep Space Nine crew tries to bypass the security measure, the worse the situation becomes.

Stardate 48423.2: While talking with Odo, Kira is approached by an interested party who would like to become better acquainted with her. Wanting nothing to do with the man, Kira tells him that Odo is her lover. However, the man will not be placated so easily. In the Gamma Quadrant, the rest of the crew, aboard the Defiant, explore a star system with no planets. However, a presence within the system peaks their curiosity. Closer examination brings out a planet from the darkness of space.

An overworked and stressed out Major Kira is relieved of duty by Doctor Bashir in the hopes that she will use the time to relax and recuperate. While beginning her vacation, the Major is approached by Commander Riker of the U.S.S. Enterprise. While taking a tour with Kira around the station, Riker asks to see the Defiant. Once on board, he stuns Kira with a phaser blast and takes control of the warship.

The Bajoran Gratitude Festival is about to begin and everyone is eagerly anticipating its commencement. While Major Kira and Chief O'Brien wait for their loved ones to arrive at the station, Odo and Jake find themselves unlucky in love. For better or worse, Odo's luck is about to change when Lwaxana Troi returns to the station.

Stardate 48481.2: The crew of Deep Space Nine proceed on the Defiant to Earth to attend a Starfleet symposium on the Gamma Quadrant. As Commander Sisko, Doctor Bashir, and Lieutenant Dax beam down, they are caught in a temporal fluxuation. They do make it to San Francisco, but they wind up there in the year 2024.

On August 30, 2024, with the Bell Riots only a few days away, Commander Sisko and Doctor Bashir are placed in a Sanctuary District in San Francisco. Unfortunately, in a heated moment, Gabriel Bell, who the riots were named for, ishuged before the Riots begin, altering the timeline. Unbeknownst to Sisko and Bashir, in 2371 aboard the Defiant, the crew witnesses Starfleet disappear before their eyes. Sisko and Bashir try to restore history by making sure that the Bell Riots continue as they should have. With the real hero dead, Sisko assumes Bell's role to make sure that the Sanctuary hostages are protected.

Stardate 48498.4: A Bajoran freighter suffering a radiation leak that caused an explosion on the ship docks at Deep Space Nine. The vessel is carrying Kai Winn and Vedek Bareil, who were on their way to begin secret face-to-face talks with the Cardassians over a peace treaty between the two worlds. Vedek Bareil, who was in initiator of the peace treaty, is severely wounded in the explosion and his chances of survival are slim. Meanwhile, Jake plans a date on the same day that he is supposed to play dom-job with Nog. Nog is all right with Jake missing out on the game, so long as Jake's date becomes a double date.

Stardate 48521.5: Returning from a frontier Bajoran colony, Major Kira and Constable Odo pick up a signal of a ship being attacked by a Maquis vessel. They trace the Maquis ship to the moon of a gas giant whose atmosphere blocks sensor readings. Venturing onto the moon in search of the Maquis, the Major is trapped in a substance that slowly begins to cover her body. On DS9, Commander Sisko is approached by Nog, who has a request to make.

Stardate 48543.2: With the help of Cardassian scientists, the crew of Deep Space Nine begins the preparations for the deployment of a subspace relay in the Gamma Quadrant. Just moments before the scientists enter the station, a Vedek arrives on DS9 to warn Commander Sisko that a prophecy has foretold the grave ramifications should the project with the Cardassians continue. As Emissary to the Bajoran people, Sisko must decide whether to follow the orders of Starfleet or the will of the Prophets.

The Ferengi Grand Nagus moves into Quark's quarter, forcing the bar owner to live with his brother, Rom. When Quark can stand no more of his brother, he goes to see the Nagus, who presents him with a revised edition of the Ferengi Rules of Acquisition. Unfortunately, the Nagus has rewritten the rules so that each one contradicts the former rule. At the same time, Doctor Bashir receives news that he has been nominated for the Carrington Award, the most prestigious award a Federation scientist can receive.

A Romulan delegation has arrived at Deep Space Nine. In exchange for using their cloaking device on the Defiant, the Romulans were offered access to all information about the Dominion. Before the delegation arrives, Chief O'Brien suffers from a plasma explosion. The radiation that he was exposed to begins to send him into the future where he see what happens to his eventual self.

Doctor Bashir is about to turn thirty years old. While talking with Garak over lunch about his upcoming birthday, Bashir is approached by Quark who has a Lethean interested in purchasing some bio-mimetic gel. Bashir tells the Lethean that it's against Federation law to purchase any and the Lethean leaves. Later, Bashir catches the Lethean going through his infirmary. The Lethean attacks Bashir with a telepathic weapon, which sends Bashir into a coma and on a trip through his mind.

Entering the operations center, Chief O'Brien asks for a bit of Commander Sisko's time. Before anyone can stop him, O'Brien places a phaser to Sisko's back and transports him off of the station. There, O'Brien explains that he is the mirror universe O'Brien. Sisko is needed to take the place of the now deceased mirror universe Sisko in order to keep the rebellion against the Alliance alive.

After lunch with Doctor Bashir, Elim Garak returns to his clothing shop where his movement within detonates a bomb located behind one of the walls. When Chief O'Brien finds material from the bomb, a rare compound that is only used by Flaxian assassins, Odo questions the only Flaxian on board Deep Space Nine. Unable to learn anything from the Flaxian, and receiving no help from Garak, Odo allows the supposed assassin to leave the station with a hidden tracking device aboard his ship.

After discovering that the Romulan Tal Shiar hadhuged the Flaxian assassin, Odo learns from an informant that the attempt on Garak's life was only a small piece of a larger puzzle. Garak and Odo journey to Cardassia to find Garak's old mentor from the Obsidian Order. Once in Cardassian space, they are met by a Romulan Warbird with Tain aboard. The Obsidian Order and the Tal Shiar have joined forces to take out the Dominion.

Doctor Bashir learns that his medical class' valedictorian, on assignment aboard the U.S.S. Lexington, is scheduled to dock at Deep Space Nine in the next few weeks. Bashir, as the salutatorian of his class, reads up as much as he can on medical texts to make sure that he is on the same ground as his competition. Meanwhile, a trip to a Bajoran antiquities museum gives Commander Sisko the opportunity to reconstruct an eight hundred year old Bajoran space vessel.

Jake Sisko's plans to set his father up with a woman ("Explorers") becomes a reality as Kasidy Yates, a freighter captain, has returned to Deep Space Nine. All that is needed is for Commander Sisko to make the first move. In Quark's, a representative from the Ferengi Commerce Authority stops by and places a "writ of accountability" sign on Quark's front door. It seems that his mother has been making profit.

Kai Winn visits Major Kira to ask her help in settling a dispute. Rakantha Province on Bajor needs soil reclamators for the start of their growing season so that they are able to start producing exportable foodstuffs that will gain them support for admission into the Federation. However, the reclamators are being held by Kira's old Bajoran cell leader during the Cardassian Occupation, Shakaar, for use on the soil in Dahkur Province.

Nog begins informal training with the Deep Space Nine crew in order to prepare himself for Starfleet Academy. Meanwhile, Jadzia Dax offers her closest friends the chance to partake in the Zhian'tara, a Trill ritual where the previous hosts are reanimated in the bodies of others so that the current Trill host can meet the former hosts of the symbiont.

Stardate 48959.1: During Commander Sisko's promotion to Captain, a Federation Ambassador informs the Captain of a possible war occurring on the heels of a coup on the Tzenkethi homeworld. Fearing attacks by the Tzenkethi on Federation colonies in their territory, Sisko prepares the Defiant for a possible war.