All Federation crew aboard Deep Space Nine begin to train for a possible infiltration by a Changling. Unfortunately, the DS9 staff is woefully unprepared as they have a hard time just tracking down Odo. As Captain Sisko spends some time with Kassidy Yates, an enormous contingent of Klingons arrive in their Birds of Prey to prepare themselves for the possibility of the Dominion coming through the wormhole.
On leave since the destruction of the Enterprise-D, Lieutenant Commander Worf is temporarily assigned to Deep Space Nine in order to find out why the Klingons have massed a fleet of warships at the station. Worf does find out that the Klingons are planning to attack Cardassia to stop what they feel is a Dominion-led coup. Captain Sisko warns General Martok that the unprovoked attack could lead to the breakdown of the treaty between the Federation and the Klingon Empire. However, Martok chooses to ignore Sisko's ultimatum and sends his fleet towards Cardassian space.
On a stormy, rain-soaked night, a woman travels through the Louisiana bayous to the residence of Jake Sisko, now an old man. An admirer of his written works, the woman wants to know why he stopped writing at such an early age. Breaking his silence, Jake tells the stranger the story of the day that he lost his dad to the infinity of time.
Stardate 49066.5: Worf begins to monitor a patron of Quark's who is a known felon. By doing so, he steps into Odo's bailiwick. Meanwhile, Dr. Bashir and Chief O'Brien are returning home after a survey in the Gamma Quadrant when they detect a possible problem with another ship. The ship's signature places it on a planet outside of the Dominion's travelled trade routes. Their shuttlecraft is then hit by an energy blast and is forced to land on the planet. Emerging from the vessel, Bashir and O'Brien become surrounded by Jem'Hadar soldiers.
Major Kira receives a call from an old friend who has found evidence that may reveal the location of the Ravinok, a Cardassian transport who was carrying Bajoran prisoners, one of whom was the Major's friend. Unfortunately for Kira, the new Cardassian civilian government receives word on the Ravinok and request that a Cardassian accompany the Major on her mission.
Stardate 49195.5: Jadzia is informed by Sisko of a Trill science team that will be arriving shortly on the station to attempt the creation of an artificial wormhole. One of the science team members is Lenara Kahn, a joined host whose symbiont had in a former host been married to Torias Dax.
Stardate 49263.5: Captain Sisko takes the Defiant into the Gamma Quadrant to meet with a race, the Karemma, who has problems with a trade agreement made with the Ferengi. While trying to reach a compromise, two Jem'Hadar ships appear and begin to attack the Karemma's ship for defying the Dominion. The ship breaks away and the Jem'Hadar follow, with the Defiant close behind.
In the Ferengi tradition of entering manhood, Nog prepares himself for Starfleet Academy by selling his boyhood possessions. At the same time, Quark acquires a ship that had been promised to him by his cousin Gaila. Suspecting that his cousin gave him a defective vessel, Quark has Rom go over the ship with a fine tooth comb. Surprisingly, Rom finds nothing wrong. To test out the ship, Quark and Rom take Nog to Earth and Starfleet Academy in Quark's new ship.
Kor, last seen in "Blood Oath", returns to Deep Space Nine and proceeds to tell great stories of his adventures with Kang and Koloth. A very fascinated Worf listens from a distance so as not to be seen by the great warrior. Still an outcast to the Klingons, he is very surprised when Kor is all to happy to meet him. Worf becomes even more surprised when Kor tells him that the Sword of Kahless, the first Klingon Emperor, has been found and Kor knows exactly where to find it.
While playing out a secret agent mission in the holosuite, Bashir is interrupted by Garak, who tags along for the excitement. Meanwhile, disaster on the Runabout Orinoco leaves Sisko, Kira, Dax, O'Brien, and Worf, caught in the transporter beam. The rest of the Ops crew are able to save their stranded compatriots by placing their pattern information in the ship's computer. Unfortunately, the computer decides that the best place to store their patterns is in the holosuite and Bashir and Garak find themselves trying to save the villains in their secret agent tale.
With no warning and no ships seen entering or exiting, the wormhole begins to open and close on its own. At the same time, a Federation meeting on Earth is the site of a grisly bombing, with 27 people killed. Evidence suggests that a Changeling was present during the explosion. Captain Sisko and Constable Odo are ordered to come to Earth to prepare the planet for a possible Dominion attack.
A world-wide power outage leads Starfleet to believe that a Dominion attack is imminent and forces Admiral Leyton and Captain Sisko to request that President Jaresh-Inyo sign over command of Earth to Starfleet. Meanwhile, Odo finds electronic evidence that an elite Starfleet Academy cadet unit, dubbed Red Squad, was brought back to Starfleet Academy just after the power failure when all of Starfleet at the time was being mobilized. When a Starfleet Admiral tells Sisko to delete the evidence from the computer system, Sisko begins to question the actions of his superiors.
First Minister Shakaar pays a visit to Deep Space Nine to begin talks for entrance into the Federation. Unfortunately, a Cardassian dissident group called the True Way has planned an attempt on Shakaar's life. With security stepped up and Odo and Worf on the job, the Minister's life seems to be in good hands. That is, until Odo notices Shakaar becoming closer to Major Kira.
Major Kira agrees to attend a conference in which the Bajorans will offer intelligence to the Cardassians on Klingon weapons and tactics. She is escorted to the remote location for the conference by Dukat, who, since he brought his half-Bajoran daughter back to Cardassia ("Indiscretion"), is no longer a Gul and has been relegated to ferrying freight and dignitaries for the Cardassian Empire.
Stardate 49556.2: For betraying Chancellor Gowron by not fighting at his side against the Cardassians ("The Way of the Warrior"), Worf's House was punished with the loss of his lands and the banishment from the Empire. While the exile damaged Worf, it hurt his brother, Kurn, most of all. Kurn shows up at Deep Space Nine seeking his brother so that Worf can perform the Mauk-to'Vor and send his brother across the river of blood into Sto-Vo-Kor and the afterlife.
Worf finds adapting to life on Deep Space Nine to be much different from that of a starship. It seems that everywhere he goes, chaos reigns supreme. In Quark's, the owner decides that the Bajoran Cleansing Ritual has cut into his profits enough to force him to cut back on the staffs' salaries. Rom tries to deal with his brother, but Quark will not listen. Forced into action, Rom decides to take Doctor Bashir's suggestion and form a union.
Keiko O'Brien's return to Deep Space Nine after a year on Bajor puts Miles in great spirits. With her arrival, Keiko brings news of a new O'Brien on the way. Meanwhile, Captain Sisko continues to remain uneasy about being the Emissary, a religious icon for an entire people. However, that is about to change when a 300 year old Bajoran light ship comes through the wormhole. The pilot of the vessel, Akorem Laan, is beamed to sick bay where he tells Sisko and Major Kira that he is the Emissary.
Stardate 49665.3: A bad dream, in which he sees a battle between Starfleet and the Klingon Empire with many lives lost, wakes Worf in his holding cell on Deep Space Nine. He has been charged by the Empire with destroying a Klingon freighter while in command of the Defiant during a battle. The Empire is seeking to extradite the Starfleet officer to Qo'noS for trial.
After twenty years of incarceration, Miles O'Brien is released by his Argrathi overseers into the hands of the Federation. However, nothing has changed much. The Argrathi means of punishment is to implant their prisoners with memories of being incarcerated for a length of time. In truth, the prisoner is only held for a while, but the prisoner remembers everything about their long time behind bars. With O'Brien released, his healing can begin... but only if he wants it to.
Jake Sisko sees his mother for the first time in nine years. Jennifer Sisko from the parallel universe visits Deep Space Nine and talks with Jake about their two different lives. While Captain Sisko attends a meeting, Jennnifer takes Jake to Terok Nor and leaves a way for Benjamin to follow them. Once there, Ben learns that the rebels, who have taken the station from the Alliance, need help in defending it before an Alliance attack fleet arrives in four days.
Looking for inspiration, Jake Sisko walks around Deep Space Nine. Watching arriving passengers, he notices a lone woman who sets her eyes upon him. Odo receives an unexpected visit from Lwaxana Troi, who is pregnant and, because of her husband's traditions, is in fear of losing her baby boy to him.
Elim Garak begins to take notice of Gul Dukat's daughter, Ziyal. He decides to become better acquainted with the only other Cardassian on Deep Space Nine. At the same time, Benjamin Sisko prepares his crew to handle the arrival of industrial replicators bound for the Cardassian colonies. The Maquis are sure to threaten the shipment and Sisko takes every threat to the replicators seriously, even the suspicion that Kassidy Yates is working for the Maquis.
While returning to the station, the crew of the Defiant come upon the aftermath of a Jem'Hadar attack on Deep Space Nine. Destroying one of the upper pylons and leaving many dead and wounded in their wake, the Jem'Hadar have mysteriously taken several electronic items. Captain Sisko and his crew head into the Gamma Quadrant with the Defiant in order to trace the attackers by their ion trail.
While on a biosurvey mission in the Gamma Quadrant, Doctor Bashir, Commander Dax, and Major Kira receive a distress signal on their Runabout from a planet. Arriving, Bashir and Dax beam down to a world of people slowly dying from an illness that begins at birth and eventually kills them, a virus given to them by the Dominion for defying them. The Federation members stay in order to help find a cure for the planet.
Quark returns from Ferenginar and informs his brother that he is dying. With little time left, Quark places his body on the Ferengi stock market in order to pay off his debts. In the Gamma Quadrant, an accident aboard a Runabout leaves Keiko O'Brien bleeding internally. With only minutes to spare, Doctor Bashir places Keiko's baby in the only other female available: Major Kira Nerys.
Stardate 49962.4: Klingon Chancellor Gowron has sent a communiqué to the Federation demanding that they stay out of Klingon territory or risk starting a war. While being set up on a date by Garak, Odo begins to succumb to a sickness that will eventually destabilize his entire body, rendering him unable to change from a liquid to a solid.