A visitor to DS9 gives Quark the earring of a legendary Bajoran POW, and Quark hands it over to Kira. Kira recognizes it as the one belonging to Li Nalas, the greatest freedom fighter in Bajoran history and legend. Kira convinces Sisko to loan her a Runabout - and Chief O'Brien as pilot - to travel to Cardassia IV. Recovering Li Nalas and a handful of other Bajorans from a forced-labor camp, Kira and O'Brien rush back to DS9. Though the Bajoran provisional government officially condemns Kira's cabalier rescue operation, the Bajorans on the station and everywhere rejoice in Li's return. Sisko hopes Li can reunite the gradually dissolving Bajoran government, which is splitting into many factions, including the extremist reactionary Circle, isolationists who mean to evict all non-Bajorans from Bajor or DS9. The Circle is, in fact, beginning to make its presence known aboard the station, as is Li Nalas, when he winds up replacing Kira as the Bajoran liaison officer on DS9.
Kira has been recalled to Bajor, and accepts an invitation from Vedek Bareil to spend some time at his monastery. There, she encounters the Third Orb, which gives her a strange vision including Dax, Vedeks Winn and Bareil, Minister Jaro, and the Bajoran Chamber of Ministers. In the meantime, as Li Nalas tries to fit into his role as DS9's first officer, the crew stumbles across evidence that the Circle is not just an isolated faction, but is instead a well-organized and surprisingly well-armed movement which is waiting in the wings to overthrow the provisional government of Bajor by force. Unknown to the Circle's members, however, they are being provided weapons by the Cardassians, who anticipate correctly that Starfleet will order Sisko and all other Federation personnel to evacuate DS9 and leave Bajor to its own political machinations, wide open for a renewed Cardassian occupation. The Circle launches assault ships to take over the station, and many of the Starfleet occupants have no choice but to stay behind and fight for their survival.
DS9 is being abandoned, and everyone from the Starfleet contingent to civilians are evacuating to various places of safety. In the meantime, Sisko and some others decide to stay and fight it out with the Bajoran assault squadrons. Kira is determined to get proof of the Cardassians' interference in Bajoran affairs to the Chamber of Ministers, even if it means walking into the assembly and showing the evidence to them herself. Li tells her where to find hidden fighter craft left over from the Cardassian occupation, and with Dax's help, Kira sets out on her mission. Bajorans General Krim and Colonel Day, along with several shiploads of soldiers, take over the station, cautious because there is no resistance. Sisko, Li, Odo, and many other crew members begin to wage guerilla warfare upon DS9's new occupants. Kira and Dax, after a quick dogfight with Bajoran assault ships, crash-land on Bajor and are rescued by Vedek Bareil, who gets them into the Chamber of Ministers with the damning evidence intact. As the Circle's popularity dissolves before the eyes of its high-ranking supporters, the Bajoran troops on DS9 are ordered to stand down - but some of them insist on bearing a deadly hatred that will cost the Bajora one of their greatest legends.
DS9 is evacuated to avoid endangering any personnel due to the passage of a plasma storm. A handful of renegades infiltrates the nearly-abandoned station with the aid of Quark, who doesn't know what they're really after. The leader of the intruders is Verad, a candidate for Trill host who was rejected by the symbiosis evalutation board as unfit for the joining, and he intends to steal the symbiont Dax. As the crew is held hostage, Bashir is coerced into performing the operation to implant Dax into Verad. As Bashir struggles to keep Jadzia alive long enough to reunite her with Dax, Sisko tries to keep the newly integrated Verad Dax talking in hope of appealing to his mentor's better nature.
A Bajoran man arrives on DS9 with his adopted son, a young Cardassian who was abandoned when his people withdrew from Bajor. This draws the attention of the Cardassian government, particularly Gul Dukat, who claims he is eager to solve the dilemma of Cardassian war orphans left behind on Bajor. DS9's resident tailor, Garak, seems to find Dukat's sudden pledge to resolve the abandoned children's situation ironic, since the boy in question is really the son of one of the civilian assembly who voted to pull the Cardassian military out of Bajoran space - one of Dukat's political adversaries. Sisko and Dr. Bashir, aided and abetted by Garak's cryptic advice, must decide the fate of the Cardassian youth, possibly deciding the end result of an internal power struggle whose combatants couldn't care less about the boy's situation.
The first Elaysian officer in Starfleet, Ensign Melora Pazlar, is assigned to DS9. Bashir and O'Brien have had to modify various passageways to permit Melora - whose low-gravity home world leaves her body reliant on a wheelchair in normal gravity - access to as much of the station as possible. In the meantime, Quark's former partner, who he once sold out to the Romulans in order to save his own skin, has finally been released by his captors and has come aboard the station to exact vengeance upon Quark. Bashir decides to make an effort to cut through Melora's oversensitivity and defensiveness in order to help her, and even discovers that there may be a way to reverse her handicap.
Grand Nagus Zek once again plans to use DS9 as the launch pad of Ferengi business opportunities in the Gamma Quadrant, and again he sees Quark as a valuable agent in securing the financial future of the Ferengi Alliance - or a scapegoat should his efforts to make commercial inroads through the other side of the wormhole fail. A newcomer to Quark's is another Ferengi named Pel, who is especially savvy to Ferengi rules of commerce and materialism - but flies in the face of the rules of traditional Ferengi customs, since Pel is a female in disguise who, in Ferengi society, could be jailed for stepping out of her house with clothes on.
Quark is hired to retrieve a list of names hidden on DS9 by a Bajoran five years ago, but when he gets curious about the list's contents, a Bajoran man enters his bar and shoots him. As Quark fights for his life in the infirmary under guard, Odo realizes that this incident is somehow linked to the murder of a Bajoran five years ago, when Odo was assigned to investigate his first crime on DS9 by Gul Dukat. The Bajoran whose murder Odo never solved turns out to be the husband of the woman who paid Quark to get the list. Five years ago, she accused Kira of the crime, claiming that the then-resistance fighter was having an affair with the woman's husband. Though the woman is currently involved in some suspicious activities, she was correct in one of those assumptions.
On the fourth anniversary of the Wolf 359 attack and the death of his wife, Commander Sisko tries to evade the painful reminder by walking around the station. On the Promenade, he meets a woman who identifies herself as Fenna, and though a spark of fascination ignites between them, she disappears without a trace moments later. The next day, despite Fenna's vanishing act, Sisko carries out his duties, including the preparation of the USS Prometheus to carry out a hazardous stellar ignition experiment under the auspices of Dr. Seyetik - whose wife, as it so happens, turns out to be Fenna...or a duplicate of her. En route to the potentially deadly site of a dead star via the Prometheus, Sisko struggles to decipher Fenna's secret.
A damaged ship emerges from the wormhole carrying four members of an unknown race from the Gamma Quadrant. The station's universal translator takes a good deal of time to decipher the aliens' language, but when it does decode their incomprehensible speech, they are able to tell Sisko and Kira that there are three million others on the other side of the wormhole, referrred to in their native Skrreean mythology as the eye of the universe, looking for Kentaana, their destiny according to legend. As it turns out, Kentaana is known in the Alpha Quadrant as Bajor, and the Skrreeans intend to emigrate there.
A new face arrives on DS9's Promenade, an open face with an apparently big heart, enough to listen through any hard luck story and comfort the person telling it. Unknown to his increasingly large number of friends, however, Martus is simply gathering information and awaiting his opportunity. When he finds a way to open an entertainment center that steals Quark's clientele, Quark begins to suspect that his luck has run out. Little does he know.
Dr. Mora Pol, the Bajoran scientist who studied Odo and first discovered that Odo is a living creature, arrives on DS9 to enlist the shapeshifter's help in another research endeavor - this time a journey into the Gamma Quadrant to investigate a world that may once have harbored beings similar in nature to Odo. Finding only the ruins of some past civilization at first, the away team also find some local flora that appear to bear some resemblance to Odo. A geological upheaval on the planet sends the members of the away team scrambling for cover from suffocating natural gases. After returning to their runabout and going back to the station, most of them wind up recovering in the infirmary recovering from gas inhalation. Only Odo appears to be unaffected, which is fortunate since something the away team has brought back from the Gamma Quadrant would appear to be lose aboard DS9 - something with abilities remarkably similar to Odo's.
Bashir and O'Brien are on attachment to a research vessel in the Gamma Quadrant, attempting to help the Kelleruns and T'lani destroy their bumper crop of biological weapons known as Harvesters. Shortly after finally discovering a means of rendering the Harvesters inert, the scientists on the alien ship are stormed by a squadron of armed troops. Only Bashir and O'Brien escape, beaming down to nearby T'lani III when they are unable to contact their Runabout. O'Brien has been infected by material from a Harvester and will die within days if he doesn't receive treatment that Bashir cannot provide without the station's medical facilities. In the meantime, Sisko and the crew have been informed that Bashir and O'Brien died in an accident aboard the research ship - but unknown to the crew, those who Bashir and O'Brien were helping in good faith are deliberately responsible for the attack.
After returning from a briefing on security measures that will be needed aboard DS9 for a summit between leaders of warring factions of the Paradans, O'Brien feels that something strange is happening, though he can't quite place a finger on what it could be. Gradually, he discovers that everything he says and does is being double-checked by Sisko and the crew. His own wife and daughter don't seem comfortable around him, and even the most innocent questions he asks are evaded by everyone. As the time of the Paradan meeting draws near, O'Brien gets desperate for answers - but everyone else on the station seems intent on stopping him.
Surveying planets in the Gamma Quadrant for potential colonization by the Federation, Sisko and O'Brien discover a world which is already inhabited by humans - to be precise, survivors of a Starfleet shipwreck who have been living on the other side of the wormhole for over a decade. Led by the charismatic Alixus, the survivors have had to rely on basic skills to stay alive, since an energy field prevents any form of technology from functioning. Alixus presses Sisko and O'Brien to abandon any hope of rescue and stay with the colony, but when the two refuse to give up so easily, they discover that their hostess is not above relying on the darkest tactics to convince them.
Detecting the emissions of a matter/antimatter reactor from an uncharted planet in the Gamma Quadrant, Dax and Odo beam down into a village whose simple inhabitants have been disappearing without a trace or any kind of explanation. At first the visitors from the Runabout are prime suspects, but once they prove that they have nothing to do with the series of disappearances, Dax and Odo are entrusted with the task of finding the guilty party. However, someone else in the village already knows the answer to the puzzle - the one person who is guaranteed not to vanish.
A Trill candidate for joining with a symbiont arrives on DS9 for observation by Dax, who will report his psychological fitness to the Symbiosis Commission on the Trill homeworld. In the course of their bumpy relationship - based on the fact that the candidate prepared himself to be in the company of Curzon Dax and not Jadzia - they pick up something unusual from the wormhole and bring it back to the station for study, not realizing that it will begin expanding rapidly until it threatens to consume the station...and the space beyond.
A damaged Cardassian starship docks at DS9 and its pilot makes an urgent request for repairs so she and her passengers can continue on their way as soon as possible. She turns out to be Natima, a member of the Cardassian anti-military underground and an old lover of Quark's from seven years ago. Her ship has been damaged while trying to escape from the Cardassians with her precious cargo: followers of her pacifist movement. Quark is overjoyed to see Natima again, but her own enthusiasm about the reunion seems much more restrained. Garak, the station's only remaining resident Cardassian, is also happy to see Natima - but only in the same way that a hunter revels at the sight of prey.
Three elderly Klingons whose days of glory passed into history and legend with the conclusion of Federation-Klingon hostilities have arrived at DS9 in search of their old friend Curzon Dax. Decades ago, after the three Klingons led a victorious assault on a ruthless enemy, their first sons were murdered in an act of revenge. The bereaved fathers made a pact, along with their mutual friend Dax, to avenge their sons' deaths. After years of searching, the murderer has been found - and they wonder if Jadzia Dax will still honor an oath of vengeance made by Curzon Dax.
A Cardassian ship is destroyed moments after leaving dock at DS9, and evidence is discovered pointing to sabotage - committed not by Bajorans, but by someone in the Federation. Gul Dukat arrives on the station, telling Sisko that things are heating up along the recently realigned Cardassian/Federation border, along which a demilitarized zone has been erected. Also present on the station is the Federation attache' to the Federation colonies on the border, Commander Hudson, who also happens to be an old friend of Sisko. Dukat and Sisko travel to one of the border colonies, witnessing a furious battle between Federation and Cardassian colonists' vessels along the way. On arrival, they discover that the human responsible for the destruction of the Cardassian vessel has been captured on DS9, interrogated and then killed, enraging the human colonists. After returning to the station, Dukat is kidnapped and taken from the station. A message is received from a group who call themselves the Maquis, claiming responsibility for the abduction. Sisko, Kira and Bashir track down the ship that must have taken Dukat from the station, and Sisko discovers that Hudson, who has voiced sympathies for the displaced Federation colonists, is the leader of the colonists in their war against their Cardassian neighbors.
The Cardassian Central Command is up in arms about the abduction of Gul Dukat, and Hudson has declared his intention to help the Maquis with all his resources. A visit from a high representative of Cardassia puzzles Sisko when he declares that Dukat is responsible for smuggling weapons into the demilitarized zone and, if returned to Cardassia, will be executed. Sisko goes after Dukat, rescuing him from the Maquis and sending a message to Hudson through renegade colonist Amaros. Dukat, as it happens, has been kept in the dark, and agrees to help Sisko prove the source of the Cardassian colonists' arms in exchange for Sisko's help in bringing Maquis violence to a halt. A captured Vulcan members of the Maquis reveals a plan to attack a hidden Cardassian weapons depot, and Sisko launches DS9's fleet of Runabouts to intercept the Maquis' two vessels. Sisko is pressured by Starfleet and Dukat to hunt Hudson down and stop him at any cost to prevent a full-scale war.
During a lunchtime disagreement with Bashir over the relative merits of Cardassian literature, Garak begins to loose his plain, simple demeanor and concerns Bashir immensely. Garak finally collapses, and Bashir discovers the source of the mysterious Cardassian's ailment - some kind of implant is connected to his brain. Quark, having been contacted by Garak to acquire something related to his problem, stumbles across the party responsible for the implant - Cardassia's Obsidian Order, a feared secret police organization which has been known to obtain information by means even darker than the Cardassian military's interrogators. Bashir risks delving into the mysteries of the Obsidian Order in a race against time to find a cure for Garak - and perhaps to learn some of his secrets.
When a Runabout's warp field doesn't completely shut off as it enters the wormhole, Kira and Bashir are detoured into an alternate universe generated by the consequences of previous travelers' interference. The station, still operating under its Cardassian name Terok Nor, and Intendant Kira Nerys lords over the station and its inhabitants with the help of first officer Garak and her Klingon cronies. Bashir is immediately forced to labor in the ore processing facility, while Kira meets her tyrannical, avaricious counterpart. Sisko and O'Brien are also to be found in this universe, as downtrodden humans living lives of virtual slavery under Kira's whip. Treachery abounds aboard the station, and Kira and Bashir can only try to play all sides against each other in order to find a way back to their own universe.
Bajor is about to elect a new spiritual leader, and Kira's lover, Vedek Bareil, is the leading candidate, having been Kai Opaka's personal choice to succeed her. After spending time with Kira on the station, Bareil prepares to return to Bajor, but the two of them first come across Vedek Winn, who is running against Bareil for Kai. Kira can barely contain her anger toward Winn, as she still blames her for an attempt made on Bareil's life. After this confrontation, Kubus, an older Bajoran, attempts to come onto the station unnoticed, but is spotted by another Bajoran, who recognizes him as a known Cardassian collaborator. As a crowd gathers, Odo arrives and arrests Kubus, while an inconspicuous Winn watches the entire scene.
While leaving for a vacation with Keiko, O'Brien encounters Boone, a former crewmate from the Rutledge. The two exchange pleasantries and O'Brien hurries off, eager to start his trip. In his haste, O'Brien fails to notice that Boone has recorded his voice. Later, as he and Keiko head toward their destination in a Runabout, they are stopped by a Cardassian vessel. To Keiko's horror, Gul Evek beams aboard and arrests O'Brien, taking him back to Cardassia Prime without telling him what he has supposedly done.
Sisko's plans for father-son bonding are ruined when Jake invites Nog to accompany them on a trip to the Gamma Quadrant. Quark insists on coming to escort his nephew, and the not-so-happy foursome wind up camping out on a primitive, uninhabited planet. Quark and Sisko argue, sending an embarrassed Nog off into the woods, with Jake chasing after him. Then, a terrified alien woman runs out of the forest, telling Sisko and Quark that she is running from a group of alien soldiers called the Jem'Hadar, who then suddenly appear and take the trio prisoner. Returning to camp to find Sisko and Quark gone, Jake and Nog set out in search of them.