Preparing for possible invasion by the Jem'Hadar, the soldiers of the Dominion, Kira determines that Deep Space Nine lacks the firepower to defend itself -- until Sisko arrives in an experimental vessel called the Defiant, a warship originally designed to fight the Borg. His plan is to travel with his officers into the Gamma Quadrant and locate the 'Founders', the unseen leaders of the Dominion, with the purpose of demonstrating the Federation's peaceful intent. If this is impossible, the presence of the Defiant with all of its weaponry will show Sisko's determination to defend against an invasion. Along for the mission is T'Rul, a Romulan with a cloaking device, which will render the Defiant invisible from the Jem'Hadar during the search. Guarding the device is Lt. Commander Eddington of Starfleet Security, who has been ordered to assume Odo's duties. Realizing he is being relieved, an angry Odo resigns. Meanwhile, Sisko coerces Quark into joining the mission because of his past dealings with the Karemma, a race that lives under Dominion rule. Odo also comes aboard the Defiant at the request of the Bajoran government, but shows to be more edgy than normal. After entering the Gamma Quadrant, T'Rul engages the cloaking device, allowing the Defiant to barely escape detection from two Jem'Hadar ships.
Odo has arrived on his home world, greeted by his fellow shapeshifters. He at last learns of his origins - he, along with hundreds of other newly-formed shapeshifters, were dispelled into the far reaches of space and genetically programmed to return home with their knowledge later, Odo is the first to make it back. But his homecoming is not without its complications - his fellow shapeshifters consider him tainted by the many years he has spent in the comapny of 'solids', and he has much to learn about his heritage. In the meantime, Sisko and Bashir, having escaped the Defiant in a shuttle, are picked up by Dax and O'Brien, who return them to DS9. Negotiations are now apparently underway between the Dominion and the Federation, but some of the proposed treaty's stipulations have sinister undercurrents, the Romulans are being excluded from the talks, though the Cardassians, Ferengi and Klingons are being welcomed, and it is revealed to Sisko that the station - and Bajor - are being handed over to the Dominion. As the Jem'Hadar being walking over the station's inhabitants, Sisko and his crew - and unlikely ally Garak - take up arms to try to take DS9 back from its new owners. Meanwhile, on the planet of the shapeshifters and unknown to all, the Founders lie in wait, conducting a terrifying experiment.
With bar business especially slow, Rom complains to Quark that their only customer, a Klingon named Kozak, says he's out of money. Quark approaches Kozak, who responds by pulling a knife. But he is so inebriated that he trips and falls on the blade, killing himself. Quark is horrified, but when the bar is flooded with patrons flocking to see what happened, he recognizes a good business opportunity and takes credit for killing Kozak in self-defense. Thrilled with his newfound popularity, he ignores Odo's warning that Kozak's family might retaliate. Sure enough, D'Ghor, Kozak's brother, soon arrives and collars Quark. A fearful Quark prepares to tell D'Ghor the truth, but learns that his life would be spared only if Kozak died honorably in battle. Thus sanctioned, Quark continues to revel in his role as a 'slayer of Klingons' until Grilka, Kozak's widow, arrives and realizes the Ferengi is lying. She takes Quark to the Klingon home world against his will, where she explains that a provision in Klingon law grants consideration to a female left without a male heir after the accidental death of a spouse. T
While experimenting with a keyboard, the musically untrained Dax inexplicably plays a melody she seems to remember from somewhere, then suddenly develops a short temper toward her fellow crew members. She soon wanders onto the Promenade, where everyone mysteriously vanishes. A robed, masked figure stands above her, then a longer version of the melody begins to play. Dax is gripped with fear as the figure appears again, blocks her path, then removes the mask, only to reveal another. She then backs into Quark, at which point the Promenade is bustling with life again -- and the masked figure is gone.
Kira is surprised when she sees records indicating that she was incarcerated at Elemspur, a Cardassian prison, ten years ago. Certain she was never at the prison, Kira tracks down a man listed as her one surviving cellmate. The stranger claims to remember Kira, but she has no idea who he is and decides to learn the truth. Kira departs for Bajor, but is kidnapped, waking up on Cardassia, where an official named Entek tells her she has been brought home. Looking in a mirror, Kira is horrified to see that she now looks like a Cardassian.
A Boslic Captain talks Quark into purchasing the wreckage of a ship that crashed in the Gamma Quadrant. Unfortunately, he ends up with much more than he bargained for when he finds a newborn alien infant hidden inside. Quark brings the baby to the Infirmary, where the child's presence reminds Sisko of his teenaged son Jake's own infancy -- and Sisko's fatherly concern now that Jake is dating Marta, a twenty-year-old Dabo girl. Bashir notices that the baby has a phenomenal metabolic rate, and the child develops so rapidly that he changes from an infant to what looks like an eight-year-old boy in a few hours.
While working in the station's ore processing unit, O'Brien and Jake accidentally activate an automated Cardassian security program, which traps the pair and Sisko in the room. Throughout the station, monitors display an old message from Gul Dukat warning of a Bajoran 'worker revolt' in the unit. Dax tries to beam out the three, but the computer requests an access code, which the Cardassians never revealed when they abandoned the station years ago. Jake crawls through a pipe and opens the hatch to the ore chute, allowing Sisko and O'Brien to get out just as lethal neurocine gas is released. Dukat's image reappears, announcing that the 'workers' have escaped, after which the doors to Ops all slam shut.
While exploring the Gamma Quadrant in the Defiant, Sisko, Dax, Bashir, and O'Brien are shocked when a planet appears where none existed before. They are contacted by a woman named Seltin, who invites them to join her people on their world for a meal. During the feast, Seltin explains that the planet, Meridian, shifts between this dimension and another, where they exist as pure consciousness. When they return to this dimension, it is as if no time has passed for them even though decades have gone by in reality. Dax is intrigued by a Meridian named Deral, who explains to her that the periods when his planet exists in this dimension are getting shorter -- this time, they will only be visible for twelve days, after which Meridian will shift back into its non-corporeal state for sixty years. Those intervals returning to Dax's dimension will soon be cut to a matter of minutes, after which the planet will become too unstable and simply cease to exist.
When Commander William Riker from the Enterprise visits the station, an intrigued Kira takes him on a tour, particularly of the Defiant. On the bridge of the docked ship, Kira uses her access code in order to show him more of the Deflant's operations. But as the ship springs to life, Riker suddenly stuns Kira with a phaser blast, then a man and a woman, Tamal and Kalita, transport aboard. Riker fakes an emergency on the warship and convinces Sisko to have it freed from the dock. The Defiant then engages warp drive and leaves the sector, at which point it is revealed that the man stealing the vessel is actually Thomas Riker, Wil Riker's duplicate, created as the result of a freak transporter accident nine years ago.
The Bajoran Gratitude Festival, an annual celebration, is about to get underway, and both Kira and O'Brien await the arrival of their loves. But while Kira's encounter with Bareil is sweet, O'Brien's long-anticipated reunion with his wife Keiko is strained -- she is exhausted and their daughter, Molly, is sick. To make matters worse, Lwaxana Troi also arrives, and immediately seeks out Odo, hoping for a romantic rendezvous, but he is uninterested. Similarly, Kira is too busy setting up for the festival to spend time with Bareil, and Keiko is too tired to enjoy her time with her husband. But at the opening festivities, Lwaxana experiences a brief headache, which Bareil and Jake seem to feel simultaneously.
En route to a symposium in San Francisco, Sisko, Dax, and Bashir are lost during transport to Earth from the Defiant. The trio materializes in San Francisco, but in the year 2024. Apprehended by a pair of policemen, Sisko and Bashir are taken to a 'Sanctuary District' -- a gated area of the city where homeless, mentally ill, and unemployed people are locked away from the rest of society. Separated from the others, Dax is found by a prominent businessman named Chris Brynner, who takes her to his office and helps her obtain the I.D. card necessary to exist in this society. Dax doesn't reveal where she comes from, but tells him that her friends are missing. Meanwhile, in the Sanctuary District, Sisko and Bashir are taken to a processing center, where no records of their existence are found. Sisko learns the date and realizes that they have arrived just days before a crucial event in history, the Bell Riots, which occurred in the area of the city where he and Bashir are now confined.
Sisko, posing as Gabriel Bell of the 21st century, takes charge of the hostage situation in the Processing Center as rioting begins within the Sanctuary District, and tells the angry residents that this is their chance to voice their grievances. Bashir reminds him that Bell is destined to die at the end of this turning point in Earth history. On the outside, Dax realizes that Sisko and Bashir are in danger and prepares to locate them. Meanwhile, Kira and O'Brien attempt transporting into different time periods to find their friends, with no success. Back in the center, Sisko convinces Webb, a decent family man, to act as their representative, but Webb is cut off from the computer interface terminal when he tries to communicate their plight. Then, police Detective Preston contacts Webb and asks to meet him.
When a serious accident nearly destroys a Bajoran transport arriving at the space station, Kai Winn manages to escape basically unharmed, but Vedek Bareil is critically injured. As Bashir operates on him while Kira worries, Winn informs Sisko that they were en route to a secret meeting to initiate peace talks with the Cardassian Central Command, and reveals that Bareil is the driving force behind the discussions. Unfortunately, Bashir is unable to save-Bareil. However, as the doctor prepares to perform an autopsy, he notices a faint indication of life. After hours of intense work on Bareil's brain, Bashir is able to revive the dead man.
While traveling in a Runabout, Kira and Odo learn that a Maquis ship has ambushed a Lissepian vessel. They pursue the attacking ship to a deserted moon, where it crashes. Kira and Odo land on the moon, which is virtually uninhabitable and rocked by seismic activity. They split up within a group of caverns where the fugitive may be hiding, but Kira soon summons Odo with a distress call. He hurries to her side to find a crystal formation growing around Kira's foot, trapping her. The crystal, which Odo cannot break, rapidly grows to just above Kira's knee. Atmospheric interference makes it impossible for him to either free her with the Runabout's transporter or send a distress signal back to the station. Odo then returns to the caverns to hear the sound of phaser blasts. Kira says that she just exchanged shots with the Maquis fugitive, but both missed. This, however, is the least of her problems -- both her legs are now entirely covered in crystal.
In the wake of the peace treaty with Cardassia, Sisko is excited about working with two Cardassian scientists who are assigned to help deploy a subspace relay in the Gamma Quadrant -- a project which, if successful, will allow communication through the wormhole for the first time. But Vedek Yarka warns that an old Bajoran prophecy predicts destruction of the wormhole, as three 'vipers' will return to their 'nest' in the sky. He deduces that the scientists are the vipers and the station must be their nest. Still, there are only two Cardassians arriving, and Sisko believes the project is too important to abandon. Later, the Cardassian scientists, Ulani and Gilora, arrive, and immediately put the crew at ease with their friendly manner. However, when they announce that another scientist will soon be joining them, Kira is concerned, believing this is the third 'viper' in the prophecy.
Zek, the Ferengi Grand Nagus, pays a visit to Deep Space Nine and moves in to Quark's quarters, where he undertakes an important project. After displacing Quark from his home, the Nagus reveals that he has been rewriting the Rules of Acquisition. Overcome with excitement, Quark and his brother Rom rush to read the volume, thrilled to have a head start on what they think will be the path to unimaginable profit. But they are shocked to read the first rule: 'If they want their money back ... give it to them.' Quark and Rom read through the New Rules of Acquisition, which have been revised to reflect qualities of kindness instead of profit and greed. Amazingly, Zek is advising his people to change their ways. Quark is mortified, especially after he later discovers that Zek has established a Ferengi Benevolent Association -- and named Rom the senior administrator of the project.
A Romulan delegation arrives to study reports on the Dominion, a privilege granted in exchange for the use of a cloaking device aboard the Defiant. Meanwhile, O'Brien, at Quark's riding out a mild case of radiation poisoning from an accident, is suddenly transported to another part of the bar, where he sees himself having a conversation with Quark. He just as suddenly returns to where he was, then falls over in pain. Bashir blames the radiation and assures O'Brien that hallucinations are a normal side effect. But when O'Brien returns to the bar five hours later, he has the same conversation with Quark that he 'hallucinated'. Dax theorizes that O'Brien's exposure to radiation could have caused him to temporarily shift five hours forward in time. Then, O'Brien experiences another timeshift -- into the middle of a brawl in Quark's between the Romulans and some Klingons.
An alien named Altovar approaches Bashir to obtain a restricted substance. The doctor refuses, prompting Altovar to later break into the Infirmary. Bashir arrives and tries to stop him, but the alien renders him unconscious with an electrical discharge. When Bashir recovers, he finds the temples of his hair graying, and the station dark and deserted. Just the most vital systems still function, and although he periodically hears strange whispering sounds, the only inhabitants found are Garak and a terrified Quark. Bashir and Garak split up in hopes of learning the fate of the others. Suddenly, his path is blocked by a forcefield, and he senses a presence coming toward him.
Sisko is abducted by a double of O'Brien, who takes him to the mirror universe that Kira and Bashir visited a year ago. This O'Brien explains that Sisko's counterpart, the leader of the Terran rebellion against the Klingon/Cardassian Alliance, has been killed. O'Brien wants Sisko to pose as his dead double and convince a Terran scientist with the Alliance to join the rebels. That scientist is Jennifer Sisko, the counterpart of Sisko's late wife. Since she is building a device that will betray the secret location of the rebels, Sisko must convince her to join them before she completes her work or the rebels will have to kill her. Unwilling to watch Jennifer die again, Sisko agrees to intervene. He meets the rebel counterparts of Bashir, Rom, Tuvok from the starship Voyager, and also Dax, who is Sisko's mistress in this universe. Only O'Brien knows that Sisko is an impostor.
A peaceful afternoon is shattered when Garak's shop is destroyed by an explosion. Although the blast initially appears to be accidental, further investigation reveals that the explosion was, in fact, rigged to look like an accident. Sisko and Odo ask Garak who might want him dead, but the Cardassian is, as always, secretive. However, Odo learns that the blast was triggered by a sensor favored by Flaxian assassins, and realizes a Flaxian named Retaya arrived that morning. Questioning Retaya reveals nothing, and Odo allows him to leave, then cancels Garak's security escort, hoping this will coerce Garak into sharing what he may know about the assassination attempt. Later, when Odo boards a Runabout to follow Retaya, Garak awaits him. Odo reluctantly agrees to let him go along as he follows the suspect. Unfortunately, they learn little about Retaya's motives -- his ship explodes just as he goes into warp.
After rejoining his former Cardassian mentor, Enabran Tain, Garak helps him in a joint mission with the Obsidian Order and the Romulan Tal Shiar. Tain has masterminded a plan to destroy the Founders -- Odo's people, who rule the Dominion -- and their homeworld. Tain, along with Colonel Lovok of the Tal Shiar, leads a fleet of cloaked Romulan and Cardassian ships into the Gamma Quadrant, commanding them from their Romulan Warbird. Garak is told to question Odo, who is being held prisoner aboard Tain's ship. However, Odo says he knows none of his people's secrets. On the station, Sisko learns of Tain's mission, and is warned by Starfleet's Admiral Toddman to prepare for retaliatory attacks by the Jem'Hadar.
Sisko returns from a trip to Bajor with the blueprint for an ancient space vessel that operates like a sailboat, using solar pressure for propulsion. According to legend, the Bajorans used these ships to explore their star system 800 years ago, even going as far as Cardassia. Sisko decides to build one himself to see if this was possible, and painstakingly recreates the vessel, determined to prove the design was spaceworthy. He hopes to have Jake join him on the adventure. After initially declining his father's invitation, Jake reconsiders, and the two prepare to depart the station. Before they do, Gul Dukat warns Sisko against putting so much stock in a Bajoran 'fairy tale' of ancient contact. Sisko feels Dukat is only interested in disproving the notion that the Bajorans, not the Cardassians, were the first people between the two races to develop interstellar travel.
In Quark's, an agent named Brunt from the Ferengi Commerce Authority -- their version of the IRS -- serves Quark with a Writ of Accountability for improper supervision of a family member. Quark and Rom's mother, Ishka, is charged with earning a profit -- an illegal activity for Ferengi women. As the family's eldest male, Quark is held responsible. He and Rom return to their homeworld, Ferenginar, where Quark must convince Ishka to confess, as required by Ferengi law. The brothers arrive at their childhood home with Brunt, but Quark is not comfortable with seeing his mother again. They are surprised to find Ishka wearing clothes, which is also illegal for Ferengi women. Brunt tells Quark he has three days to get his mother to sign a confession, then leaves. Later, Ishka confirms over dinner that she broke Ferengi law by investing a portion of her monthly stipend from Quark, earning a meager three bars of latinum in the process. Still, she refuses to confess, which angers her oldest son.
When the First Minister of the Bajoran Provisional Government dies, Kai Winn is appointed to his duties and about to be formally elected. Later, Winn approaches Kira with a special request. A group of farmers in Kira's home province refuse to return some soil reclamators that Winn needs for Bajor's recovery efforts in Rakantha Province. Their leader, Shakaar, also led Kira's resistance cell during the occupation, so Winn wants Kira to convince him to return the property. Kira is reluctant to go up against a friend, but agrees to do it for the good of Bajor. Kira returns home and finds Shakaar, who calmly tells his side of the story: he only received the reclamators two months before, after a three-year wait, and was told that he and fellow farmers Furel and Lupaza would have their use for a year. But when Winn took over, they were ordered to return them immediately. Since the Rakantha project is geared toward farming products for export, while Shakaar's farmers are trying to feed their people, he sees his project as far more important. Kira encourages him to meet with Winn, hoping they can compromise.
Jadzia Dax prepares for her zhian'tara, the Trill Rite of Closure. During the ritual, Jadzia will meet Dax's previous hosts, which will be accomplished by transferring the memories of each into someone's body. Sisko, Kira, Bashir, Odo, Quark, O'Brien, and Leeta agree to participate, and a Guardian performs the ceremony. Kira undergoes the transference first, becoming Lela, Dax's initial host. The Guardian leaves Jadzia alone with Lela, who exhibits several traits Dax has inherited. So do subsequent hosts O'Brien/Tobin and Leeta/Emony. Quark experiences some discomfort hosting a female entity, Audrid, while Bashir/Torias regrets that an accident ended his life too soon. Jadzia then prepares for her most difficult meeting--with Joran, who once committed murder. Sisko has volunteered to host his memories, and the transference is conducted inside a holding cell.
During a party celebrating Sisko's promotion to Captain, Admiral Krajensky takes him aside and quietly reveals that there has been a coup on the Tzenkethi homeworld that could threaten Federation colonists. Sisko and his crew are to take the Defiant and Krajensky to this sector. Soon after departing, they receive a distress signal from a colonist indicating that Barisa Prime is under attack from the Tzenkethi. The signal then goes dead -- the colony has apparently been destroyed. The crew sets course for Barisa Prime, but when Sisko tries to notify Starfleet Command, power fluctuations in the ship's communications circuitry prevent it. O'Brien and Dax go to work on the problem, and discover strange alien devices attached to almost every critical system throughout the ship. They determine that there is a saboteur aboard. Dax scans each member of the crew, and when she gets to Krajensky, he suddenly morphs into a Changeling and escapes.