Recently promoted to Colonel, Kira continues to oversee Deep Space Nine while Captain Sisko is away on Earth. The Dominion War continues to go badly for the Federation and a Romulan delegation is invited to the station to coordinate efforts. Away for the past three months, Sisko waits in his father's establishment in New Orleans, waiting for a message from the Prophets. He finally receives one and is shown an image of a woman in the sand.
Stardate 52152.6: Accompanied by Doctor Bashir, Chief O'Brien, and Quark, Worf sets off on General Martok's Bird of Prey on a glorious mission to attack a Dominion shipyard. Using the element of surprise to destroy the base, Worf hope that this mission will help Jadzia reach Sto-Vo-Kor. On Deep Space Nine, the Romulan armament on one of Bajor's moons has been found out and Major Kira blockades the moon so that no Romulans attempt to land on the surface. On Tyree, Captain Sisko, his father, son, and Ezri Dax, look for the message that the Prophets have been guiding Benjamin towards.
Although it has only been a few days she stepped foot on the station, Ezri Dax has many memories of Deep Space Nine, both good and bad. The problem, however, is that she reminds almost everyone of Jadzia. Due to this, Ezri has decided to leave the station and return to her previous assignment as ship's counselor. Just before she leaves, she is ordered by Captain Sisko to look in on Garak, who has had several claustrophobic panic attacks.
The Federation starship T'Kumbra, staffed with an all Vulcan crew, has docked at Deep Space Nine for repairs. Its Captain is Solok, who has an intense rivalry with the Captain of DS9. Since the holosuites on the T'Kumbra are down, Solok requests the use of the station's holosuites. In doing so, he puts forth the challenge to Sisko and his staff to best his Vulcan athletes in an old Terran form of competition: Baseball.
Doctor Bashir's four genetically-altered colleagues - Jack, Sarina, Patrick, and Lauren - return to Deep Space Nine so that Bashir can help Sarina regain her ability to process information around her, allowing her to communicate with others. While the doctor does not have the entire procedure ready for use, his three friends are more than willing to help Sarina in any way they can.
Needing a stabilizer on the Defiant, Captain Sisko orders Chief O'Brien to have part in place on the ship when he returns in three days. Unfortunately, O'Brien won't be able to procure the item for three weeks. Overhearing the conversation with the Captain is Nog, who offers to use a bit of his Ferengi sense of commerce to find the stabilizer for the Chief in three days. Elsewhere, Odo receives a message from his Cardassian contact, long thought dead, to rendezvous with him at their usual location. While there, Odo discovers that his contact is in fact dead. In his place stands Weyoun, who has decided to defect to the Federation.
Planning a sweeping attack with five Klingon vessels against a Dominion installation, General Martok readies his troops for battle. Much to his chagrin, he learns that Worf wishes to have the old Klingon Kor, who the Empire no longer has a place for, join the fleet in a command post. Martok refuses, but Worf uses his influence to make Kor an officer, where the Dahar Master will join the calvary aboard Martok's flag ship as third in command.
The Defiant heads to AR-558, a former Dominion communications array now under Federation control. The array, however, isn't giving ups its secrets too easily and all attempts to link up with the array have proven fruitless. With subspace mines set up around the asteroid and Jem'Hadar soldiers continuing to lay siege to the rock, coupled with Federation forces that have been holding the array for five months, the Defiant crew find a demoralized force in place. When the Jem'Hadar attack yet again, Sisko elects to stay behind with his team in order to hold the ground.
Major Kira receives a former teacher of hers, now a Vedek, who had been on sabbatical from the University of Bajor. Always travelling and seeking answers, the Vedek brought the Major something that she may find interesting. When she unwraps the gift, she is transported to Empok Nor, Deep Space Nine's sister station, long thought abandoned by the Cardassians. Now, a group of Bajorans have settled there. Worshipping the enemies of the Prophets, the Pah-Wraiths, they now follow their Gods under a new leader: Dukat.
Lieutenant Nog returns to Deep Space Nine after being fitted with a new leg after he lost his limb against the Jem'Hadar at AR-558 ("The Siege of AR-558"). Tired out from all the talking that he has had to do with Federation counselors, Nog wants nothing more than to return to duty. His leg, however, refuses to cooperate.
Julian notifies Captain Sisko that Chief O'Brien has been out of touch for three days. The Chief had been searching for the wife of a former Orion Syndicate member who he had helped capture ("Honor Among Thieves"). His last known location was New Sydney, where, coincidentally, Ezri's mother has quite a bit of influence since she runs a mining operation in the sector. After three years away, Ezri finally returns home to see her family and learn whatever she can about the whereabouts of O'Brien.
While Quark prays to the Grand Exchequer to allow him prosperous business and to see his dream of being with Ezri come to fruition, he receives a visit from a very different Ezri. Unfortunately for Quark, this isn't Ezri Dax, and she isn't here on a social call. The Grand Nagus, who has been missing for some time, greets Quark from a message tube, and goes on to say that he tried to open negotiations for trade with the Mirror Universe's Alliance. However, the venture is in jeopardy unless Quark is able to smuggle a cloaking device into the Mirror Universe. Should he fail, the Nagus will be meeting the Grand Exchequer in person.
After a night of celebrating his successful mission aboard the Defiant, a Lieutenant Junior Grade is killed with a shot through the heart. Later, another Starfleet officer is found cuddled. In both instances, the weapon used to hug the victim fired a projectile round, not seen since the advent of phaser rifles. Ezri Dax, who had become acquainted with the Ensign, finds herself dreaming about the Dax host who had been found guilty of hug. That former host, Joran Belar, is trying to reemerge through Ezri to help find the hugger.
Returning from a conference, Chief O'Brien and Constable Odo are paid a visit by a Changeling. However, the Changeling calls himself a Metamorph. He, like Odo, was one of the one hundred shape-shifters sent out by the Founders at an early age in order to experience other species' ways of life. The Metamorph has been trying to return home ever since. Luckily, Odo is the first shape-shifter that the Changeling encountered.
Visiting Vic before they enter their Alamo holosuite program, Doctor Bashir and Chief O'Brien are entertained by the hologram to put them in the mood before they make their last stand at the mission. However, before Vic can finish his song, his holosuite setting is changed to a mafia-type casino run by one of the local bosses, who has just purchased Vic's old place of business. Unable to turn the program off, Bashir and O'Brien leave with Vic in order to figure out how to bring back Vic's former haunts.
The continuing war with the Dominion begins to strain relations between the Klingons and the Romulans. Meanwhile, the Federation is more than happy to accomodate their new Romulan friends. However, some within the Federation are not happy about this. One of them is Luthor Sloan, Director of Section 31. Reaching out to his newest recruit, he assigns Doctor Julian Bashir to a clandestine mission.
Stardate 52576.2: On a visit to Bajor, Captain Sisko is taken for a trip to Kendra Provice, where he eyes some land that is so beautiful to him, he purchases it, bringing himself one step closer to living on Bajor. Meanwhile, the Colonel brings word that the I.K.S. Rotarran and I.K.S. Koraga had been attacked in the Badlands by the Dominion. The Koraga is destroyed and only six escape pods are retrieved. The Captain of the ship, Lieutenant Commander Worf, is not among the survivors found.
Sisko has been told by his mother that he must walk in the path that the prophets have laid out for him, which may mean not marrying Kasidy. Kai Winn visits Benjamin and he tells her a bit about his vision. Once she leaves, she receives her first vision and is told that the Sisko has strayed from the path and that she must put Bajor on the right path again.
A generous offer has been made by the Dominion to the Breen Confederacy. With a new alliance about to be created, the Dominion's leaders, the Founders, are confident that the new treaty between the two great empires will bring an end to the Federation once and for all. However, Legate Damar is not very happy with the arrangement. While he is the leader of Cardassia, his rank is merely ceremonial. The Dominion really controls the Cardassian Union, and Damar cannot see anything good about this new treaty.
Helped by Legate Damar escape from the Dominion, Ezri and Worf have returned to Deep Space Nine. Unfortunately, they have little to report to Sisko about the new Dominion-Breen alliance. The only thing that is made clear is the message that Captain Sisko receives moments later: The Breen have attacked Earth.
The Battle of Chin'toka has decimated the Federation. Of all starships assigned to the campaign, only one survived the Breen onslaught. The Klingon Bird of Prey that did survive has allowed the Federation-Klingon-Romulan Alliance to come up with a partial way of defending themselves. Fortunately for them, the Cardassians have risen up against their former allies, buying Starfleet and the Romulans time to develop defenses agains the Breen's weapons. In an effort to help the Cardassians, Sisko sends his best officer to aid them in throwing off their Dominion oppressors: Colonel Kira Nerys.
While Colonel Kira lectures the Cardassians on their tactics, Odo returns from a successful mission agains the Dominion. Taking a break, he rests his now weakened body. Unknown to him, he was infected long ago by Section 31 and now it's only a matter of time before he succumbs to the illness. On Deep Space Nine, Worf tries to persuade Chancellor Gowron to stop his offensives that are taking the lives of countless Klingon warriors.
Stardate 52645.7: With Odo knocking at death's door, scant time remains to find a cure. In an effort to lure Section 31 out of hiding to obtain the vaccine, Doctor Bashir and Chief O'Brien have gone behind Captain Sisko's back. Now, telling him about their plan, Doctor Bashir informs Sisko that Section 31 is the only hope that Odo has left.
Stardate 52889.3: The Federation has started to catch up with the new Dominion-Breen weaponry. Arriving from the Utopia Planetia Fleet Yards is the U.S.S. Sao Paulo, a Defiant-class warship with the most up-to-date specs on Breen weaponry. With the arrival of the Sao Paulo, the Federation is once again back in the game. On Cardassia Prime, Colonel Kira, Garak, and Legate Damar attempt to bring more of the Cardassian military into their force, only to be caught in a trap. The three transport to the surface in an out-of-the-way place, but they see that they are in trouble. Their Jem'Hadar vessel is destroyed high above them, they are left stranded deep in enemy territory.
In the first part of the final episode of the series we find the Alpha Quadrant Alliance working together to prepare a final invasion of Cardassia. With their limited resources they work together to find a possible way to defeat the Dominion and the Breen.
Benjamin is visited once more by his mother Sarah in a vision with news that his role as Emissary may soon end.
In part two of the series finale the Caradassian Rebellion reaches Dominion headquarters leaving Weyoun and the Female Changeling to realize that the end of their reign of terror may be near.
The Federation Alliance wins their final battle against the Dominion and Breen with some heartbreaking consequences.