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Season 1 (January 3, 1993 - June 20, 1993)
- Emissary: Benjamin Sisko, a Starfleet commander and veteran of the Battle of Wolf 359, is assigned to Deep Space Nine, a captured Cardassian space station near Bajor. The discovery of a stable wormhole leading to the Gamma Quadrant, and the incorporeal aliens worshipped by Bajorans as gods living within it, forever changes Sisko's destiny. January 3, 1993
- Past Prologue: As Bashir becomes acquainted with a Cardassian "tailor" named Garak, a Bajoran terrorist tied to Kira's past attempts to drive a wedge between the Federation and Bajor. January 10, 1993
- A Man Alone: Odo is accused of murdering a Bajoran criminal, causing unrest among the station's Bajoran citizens. January 17, 1993
- Babel: A mysterious plague sweeps across the station, rendering people incapable of speaking coherently. January 24, 1993
- Captive Pursuit: O'Brien finds himself protecting an alien from the Gamma Quadrant who is being pursued by hunters. January 31, 1993
- Q-Less: Vash, an adventurous archaeologist, arrives on the station. Unfortunately for everyone aboard, she is being pursued by Q, the interdimensional troublemaker. February 7, 1993
- Dax: A request for extradition is made against Jadzia Dax for a thirty year old murder case, in which Curzon, the Dax symbiont's previous host, is a prime suspect. February 14, 1993
- The Passenger: An alien fugitive is brought aboard the station in a comatose state. Little does anyone realize, the fugitive has transferred his consciousness to someone else. February 21, 1993
- Move Along Home: After attempting to cheat ambassadors from the Gamma Quadrant, Quark finds himself playing a dangerous game in which the rules are never explained, and the lives of Sisko and his crew are at stake. March 14, 1993
- The Nagus: The sudden demise of Grand Nagus Zek, leader of the Ferengi Alliance, thrusts Quark into the Nagus's position of power, with all of the dangers that come with it. March 21, 1993
- Vortex: A Gamma Quadrant fugitive approaches Odo with an enticing offer: in exchange for his freedom, he’s willing to tell Odo about others of his kind. April 18, 1993
- Battle Lines: Sisko, Bashir, Kira, and Kai Opaka find themselves stranded on a planet where the inhabitants are locked in an eternal war and no one can die. April 25, 1993
- The Storyteller: O'Brien finds himself in the unenviable position of fending off a strange energy being threatening a Bajoran settlement, and the only way to protect the people is to recite an old story. May 2, 1993
- Progress: Kira is sent to oversee the evacuation of a Bajoran colony situated on a moon that’s about to become uninhabitable. She has her work cut out for her, as one ornery farmer refuses to leave. May 9, 1993
- If Wishes Were Horses: A spatial anomaly has given life to the imaginations of the station's inhabitants, as everyone and everything from fairy tale villains to baseball stars of yesteryear appear and cause havoc. May 16, 1993
- The Forsaken: The station finds itself crippled by an alien computer during a visit from the Betazed ambassador Lwaxana Troi. May 23, 1993
- Dramatis Personae: A psychic imprint from a civilization that self-destructed forces itself upon the station's crew. May 30, 1993
- Duet: Kira suspects that a Cardassian infected with an illness that can only come from Bajoran labor camps may be an infamous war criminal. June 13, 1993
- In The Hands Of The Prophets: Tensions flare on the station as Vedek Winn, a dogmatic leader of Bajor's faithful, takes umbrage with Keiko O'Brien's secular teachings of the wormhole. June 20, 1993
Season 2 (September 26, 1993 - June 12, 1994)
- The Homecoming (first of a three-parter): As Kira aids a Bajoran Resistance hero trapped in a labor camp, a group of extremists known as "the Circle" call for all non-Bajorans to leave their homeworld. September 26, 1993
- The Circle (second of a three-parter): As the Circle advances their agenda, Sisko and Odo must discover the force leading their coup of the station. October 3, 1993
- The Siege (third of a three-parter): Sisko finds himself in a desperate struggle to retake the station from the Circle as Kira and Jadzia hold evidence of the true source of the extremists' martial might. October 10, 1993
- Invasive Procedures: A trill who had been denied the chance to have a symbiont implanted in him kidnaps Jadzia to take the Dax symbiont for himself, endangering Jadzia's life. October 18, 1993
- Cardassians: A group of Cardassian war orphans arrive on the station, piquing Bashir and Garak's curiosity. October 25, 1993
- Melora: Bashir meets and falls for a Starfleet officer whom he helps adapt to life in normal gravity as Quark's former associates threaten him. October 31, 1993
- Rules of Acquisition: Quark is given a task by the Grand Nagus; to open negotiations with a planet discovered in the Gamma Quadrant that could bring profit to the alliance. November 7, 1993
- Necessary Evil: Odo investigates a five-year-old cold case that is tied to a recent attempt on Quark's life. November 14, 1993
- Second Sight: Sisko finds himself falling in love with a woman who arrived on the station, but there is much more to her than meets the eye. November 21, 1993
- Sanctuary: A group of refugees come from the wormhole in search of their homeworld. November 28, 1993
- Rivals: A con-artist opens a new bar on the station, threatening Quark's business. January 3, 1994
- The Alternate: The Bajoran scientist who first discovered Odo comes with evidence that the Constable is not alone in the universe. January 9, 1994
- Armageddon Game: O'Brien and Bashir aid in efforts to disarm two warring factions' biological weapons. Unfortunately for them, the powers that be decide that they know too much. January 30, 1994
- Whispers: O'Brien returns to the station, only to find everyone aboard acting bizarrely. February 6, 1994
- Paradise: Sisko and O'Brien find themselves on a planet where human colonists live without technology, a way of life they are determined to keep by any means necessary. February 13, 1994
- Shadowplay: Odo and Jadzia investigate a Gamma Quadrant colony where people have begun to vanish under mysterious circumstances. February 20, 1994
- Playing God: A protouniverse has begun to materialize, threatening the station and the entire Bajoran sector. February 27, 1994
- Profit and Loss: Quark reunites with an old flame, a Cardassian professor...but is she still the same woman he remembers? March 20, 1994
- Blood Oath: A group of Klingons seek out Curzon Dax to help them carry out an act of vengeance. Jadzia, Curzon's successor, decides to help fulfill an old promise. March 27, 1994
- The Maquis Part I: Tensions flare between the station and the Cardassians when a freighter is destroyed by a Bajoran insurgent group. April 24, 1994
- The Maquis Part II: Sisko must stop a war from starting by rescuing Gul Dukat from the Maquis. May 1, 1994
- The Wire: Garak's life is endangered by a brain implant he was given during his days as a spy. Bashir must try to save Garak before the decaying implant kills him. May 8, 1994
- Crossover: Kira and Bashir find themselves in an alternate universe, where the Bajorans rule over the Alpha Quadrant with an iron fist, and Kira's counterpart reigns as a brutal dictator. May 15, 1994
- The Collaborator: Kira falls for Vedek Bareil, a spiritual leader for Bajor. Unfortunately for them, Bareil is accused of aiding the Cardassians during the occupation. May 22, 1994
- Tribunal: O'Brien is arrested by the Cardassians on charges of aiding the Maquis. Is there any chance of saving him from execution in a legal system where the accused is always declared guilty? June 5, 1994
- The Jem'Hadar: Sisko, Quark, Jake, and Nog go camping, only to find themselves in the crosshairs of the Dominion and their footsoldiers, the Jem'Hadar. June 12, 1994
Season 3 (September 26, 1994 - June 19, 1995)
- The Search Part I: At the helm of the Federation's new warship, the Defiant, Sisko leads the charge to find the Founders, the rulers of the Dominion. September 26, 1994
- The Search Part II: As Odo discovers that he is of the same race as the Founders, Sisko must stop Starfleet from giving into the Dominion's demands. October 3, 1994
- The House of Quark: The accidental death of a drunk Klingon finds Quark thrust into a game of Klingon intrigue as the widow suddenly marries him. October 10, 1994
- Equilibrium: Jadzia finds herself plagued with hallucinations brought on from memories from a previous host of the Dax symbiont October 17, 1994
- Second Skin: Kira awakens to find her appearance changed to look like a Cardassian, and her captors attempting to convince her that she is one of them. October 24, 1994
- The Abandoned: Quark accidentally buys a Jem'Hadar child, whom Odo takes under his wing. October 31, 1994
- Civil Defense: An old defense system on the station from the Cardassian occupation activates, threatening to kill everyone aboard unless Sisko and his crew can shut it down. November 7, 1994
- Meridian: Jadzia enters into a relationship with a scientist on a world where the inhabitants live in a state of flux between the physical universe and a realm of pure energy. November 14, 1994
- Defiant: Commander William T. Riker of the USS Enterprise accompanies Kira to inspect the Defiant, only to incapacitate Kira and commandeer the warship for the Maquis! November 21, 1994
- Fascination: Lwaxana Troi returns to the station, and trouble soon follows as the inhabitants are overcome by sudden feelings of infatuation for one another. November 28, 1994
- Past Tense Part I: Sisko, Bashir, and Dax find themselves thrust into the past, during a dark period of Earth's history where the destitute are force to live in impoverished "sanctuaries". January 2, 1995
- Past Tense Part II: Finding himself in the role of the man who helped to reform Earth's "sanctuary" cities, Sisko must ensure history stays on its course as O'Brien and Kira try to retrieve him, Bashir, and Dax. January 9, 1995
- Life Support: Vedek Bareil is gravely injured just days before the signing of a peace treaty between Bajor and Cardassia. Can Bashir keep him alive long enough to see the treaty signed? January 30, 1995
- Heart of Stone: As Nog tries to convince Sisko to let him enter Starfleet, Kira becomes trapped in a rock formation that is encasing her, bringing Odo's feelings for her bubbling to the surface. February 6, 1995
- Destiny: An attempt to establish communications across the wormhole threatens the shaky alliance between the Federation, Bajor, and Cardassia as a prophecy of doom comes to light. February 13, 1995
- Prophet Motive: Grand Nagus Zek is poised to implement new policy in the Ferengi Alliance that promote generosity and philanthropy, leading Quark to believe his people's leader has lost his mind. February 20, 1995
- Visionary: What was thought to be a simple case of minor radiation poisoning finds O'Brien jumping between the present and a future where the station is destroyed and everyone aboard is dead. February 27, 1995
- Distant Voices: Bashir is rendered comatose by an alien who locks his consciousness inside his own mind and torments him. April 10, 1995
- Through the Looking Glass: Sisko finds himself in the mirror universe, meeting its version of Jennifer, whom he must convince to join the Terran Rebellion for her own survival. April 17, 1995
- Improbable Cause (first of a two-parter): Odo finds a bomb in Garak's tailor shop, threatening to destroy the station. April 24, 1995
- The Die Is Cast (second of a two-parter): Cardassia and Romulus join forces as Sisko must rescue Odo. May 1, 1995
- Explorers: Sisko and Jake embark on a journey from Bajor to Cardassia, using a pre-warp drive Bajoran vessel. May 8, 1995
- Family Business: Quark finds himself in hot water as Ferengi authorities accuse his mother of a most grievous crime: earning profit as a female. May 15, 1995
- Shakaar: A group of Bajoran insurgents Kira used to be a member of steal farming equipment, forcing her into a difficult position as Kai Winn schemes to take the seat as Bajor's leader. May 22, 1995
- Facets: Jadzia participates in a ritual that awakens the consciousnesses of the Dax symbiont's previous hosts. June 12, 1995
- The Adversary: After being promoted to captain, Sisko undertakes a patrol in the Defiant that goes awry when a changeling saboteur plots to destroy the ship from within. June 19, 1995
Season 4 (October 2, 1995 - June 17, 1996)
- The Way of the Warrior: As Commander Worf is welcomed onto the station, relations between the Klingon Empire and the Federation deteriorate, forcing Worf to pick a side. October 2, 1995
- The Visitor: Far into the future, an elderly Jake Sisko recounts to a visitor his attempts to rescue his father after an accident traps Ben Sisko in subspace. October 9, 1995
- Hippocratic Oath: Bashir and O'Brien find themselves attempting to help a group of Jem'Hadar acquire Ketracel White, a narcotic they are all born addicted to. October 16, 1995
- Indiscretion: Kira and Dukat are forced to set aside their differences to track down a crashed Cardassian freighter carrying Bajoran prisoners. October 23, 1995
- Rejoined: Dax is reunited with Kahn, a symbiont she was once married to through another host. October 30, 1995
- Starship Down: Sisko must come to the aid of a ship targeted by the Jem'Hadar. November 6, 1995
- Little Green Men: Quark, Rom, and Nog are sent back into the distant past of 1940's Earth, where they are mistaken for alien invaders. November 13, 1995
- The Sword of Kahless: Jadzia and Worf uncover a weapon in the Gamma Quadrant that was used by the mythological Klingon warrior Khaless. November 20, 1995
- Our Man Bashir: Bashir partakes in a holosuite program where he acts out the tales of a dashing superspy, only for a transporter accident to replace the characters with his co-workers. November 27, 1995
- Homefront (part one): Changelings have infiltrated Earth, and Sisko is recalled to help protect his homeworld from Dominion influence. January 1, 1996
- Paradise Lost (part two): As paranoia over the changeling threat grips Earth, Sisko and Odo must stop a Starfleet admiral from using the chaos to conquer the planet. January 8, 1996
- Crossfire: Romance blossoms between Kira and a First Minister who fought in the Bajoran resistance, and Odo must come to terms with his feelings for her. January 29, 1996
- Return to Grace: The Klingons destroy an outpost with Cardassian and Bajoran diplomats aboard, forcing Kira and Dukat to work together to confront them. February 5, 1996
- Sons of Mogh: Worf's younger Klingon brother Kurn comes to the station, bereft of his family's honor, in the hopes that Worf will kill him and end his suffering. February 12, 1996
- Bar Association: Rom leads Quark's workers in forming a union demanding better wages and working conditions, attracting the attention of the Ferengi authorities. February 19, 1996
- Accession: An old Bajoran ship emerges from the wormhole, carrying a man who claims to be the Emissary. February 26, 1996
- Rules of Engagement: Worf is accused of destroying a ship carrying Klingon civilians, with the Empire calling for his extradition. April 8, 1996
- Hard Time: O'Brien is convicted of espionage by an alien race and sentenced to have the memories of twenty years in prison implanted in his mind, torturing him. April 15, 1996
- Shattered Mirror: The Mirror Universe's Jennifer Sisko appears in the main universe, hoping to lure Jake to her universe so he can help the Terran Rebellion put the finishing touches on their own Defiant. April 22, 1996
- The Muse: As Jake falls under the thrall of an older alien woman who feeds on his creative thoughts, Lwaxana Troi returns to the station, carrying a child and asking Odo to marry her so she can retain custody. April 29, 1996
- For The Cause: Sisko's new girlfriend, Kasidy Yates, is accused of aiding the Maquis. Meanwhile, Garak develops a fondness for the station's newest inhabitant: Ziyal, the half-Bajoran daughter of Gul Dukat. May 6, 1996
- To the Death: Jem'Hadar soldiers ambush the station, leading Sisko and his crew on a mission to destroy a gateway that allows the Jem'Hadar to infiltrate anywhere. May 13, 1996
- The Quickening: The Dominion infects a race of aliens with an incurable plague, and Bashir must find a way to help them survive. May 20, 1996
- Body Parts: Quark learns that he is dying and offers his future remains to the highest bidder. When he is expected to survive, however, his faith in Ferengi politics will be put to the test. June 10, 1996
- Broken Link: As the Federation and the Klingon Empire are on the precipice of war, Odo finds himself unable to shapeshift, threatening his life unless he returns to the Founders for a cure. June 17, 1996
Season 5 (September 30, 1996 - June 16, 1997)
- Apocalypse Rising: A changeling is posing as the leader of the Klingons' armies, and Sisko and his crew must infiltrate their ranks to oust the impostor. September 30, 1996
- The Ship: Sisko discovers a crashed Jem'Hadar fighter, and must protect it from those that would take it to use against the Federation. October 7, 1996
- Looking for par'Mach in All The Wrong Places: Quark's Klingon ex-wife returns to the station, and Worf's jealousy eventually leads to him entering into a relationship with Jadzia. October 14, 1996
- Nor the Battle to the Strong: Jake accompanies Bashir to the frontlines of the war with the Klingons in the hopes of finding a news story, only to learn firsthand how terrifying war is. October 21, 1996
- The Assignment: O'Brien's wife Keiko is possessed by a Pah-wraith, a malevolent spirit from Bajoran mythology, and threatens to kill her if O'Brien doesn't help it destroy the Prophets. October 28, 1996
- Trials and Tribble-ations: Sisko must explain to Starfleet what exactly he and his crew were doing back in the 23rd century, aboard the original USS Enterprise with Captain James T. Kirk. November 4, 1996
- Let He Who Is Without Sin...: A trip to Risa goes awry when Worf finds his relationship with Jadzia tested amidst an extremist group attempting to sabotage everyone's fun. November 11, 1996
- Things Past: Sisko, Odo, Dax, and Garak are thrust seven years into the past, in the roles of Bajorans who were executed for an attempt on Gul Dukat's life. November 18, 1996
- The Ascent: Odo and Quark are forced to set aside their differences and help each other when they are trapped on a hostile world. November 25, 1996
- Rapture: As Bajor is poised to enter the Federation, Sisko discovers an ancient city, and with it, visions from the Prophets of the future. Those same visions, however, are endangering his life. December 30, 1996
- The Darkness and the Light: Kira's old friends in the resistance are being murdered, one after another, by an enemy from her past. January 6, 1997
- The Begotten: Odo discovers an infant changeling and attempts to bond with it. Kira gives birth to Miles and Keiko's baby Kirayoshi. January 28, 1997
- For the Uniform: Michael Eddington has betrayed Starfleet for the Maquis, and Sisko must pursue him. February 3, 1997
- In Purgatory's Shadow (part one): Garak and Worf discover evidence that a deceased Cardassian spymaster may still be alive, only to find them in company with the Klingon general Martok. February 10, 1997
- By Inferno's Light (part two): Worf and Garak must escape from a Dominion prison as Sisko and his crew defend the station from invasion. February 17, 1997
- Dr. Bashir, I Presume: Dr. Zimmerman enlists Bashir's aid in making a new medical hologram, and in so doing, inadvertently discovers his deepest, darkest secret. February 24, 1997
- A Simple Investigation: Odo must protect a woman who is targeted for death by a criminal organization, and ends up falling for her. March 31, 1997
- Business as Usual: With no latinum to his name, Quark decides to enter into the dangerous world of arms dealing with his cousin. April 7, 1997
- Ties of Blood and Water: Kira must help a Cardassian who is aiding dissidents on his homeworld live long enough to make a testimony. April 14, 1997
- Ferengi Love Songs: Quark returns to his homeworld and discovers something most scandalous: his mother and the Grand Nagus are romantically involved. April 21, 1997
- Soldiers of the Empire: Worf is made Martok's first officer on a Klingon bird-of-prey, and he finds himself conflicted between loyalty to his commander and his crew mates. April 28, 1997
- Children of Time: Sisko and his crew find themselves stranded on a planet inhabited by their distant descendants. May 5, 1997
- Blaze of Glory: Sisko and Eddington must set aside their differences to prevent a Maquis missile from destroying Cardassia. May 12, 1997
- Empok Nor: O'Brien leads a salvaging operation on an old and abandoned Cardassian space station...but something sinister is hidden onboard. May 19, 1997
- In the Cards: As the Dominion and Bajor enter into a non-aggression pact, Jake and Nog try to get their hand on a vintage baseball card. June 9, 1997
- Call to Arms: The Dominion War begins in full earnest as Dukat launches an all-out invasion to retake the station. June 16, 1997
Season 6 (September 29, 1997 - June 17, 1998)
- A Time to Stand (part one): Sisko captains a captured Jem'Hadar ship on a mission to deprive the Jem'Hadar of Ketracel White in an effort to turn the war against the Dominion around. September 29, 1997
- Rocks and Shoals (part two): Sisko's crew and a Jem'Hadar ship both crash-land on a planet and must survive as Kira is forced to work for the Dominion on the recaptured Deep Space 9. October 6, 1997
- Sons and Daughters (part three): A new batch of young soldiers are brought onboard Martok's ship, including Alexander Rozhenko, Worf's estranged son. October 13, 1997
- Behind the Lines (part four): Kira and a few insurgents work to subvert the Dominion's efforts to disarm the minefield preventing any more ships from entering the Alpha Quadrant. Hindering their efforts is one of the Founders, who seduces Odo and convinces him to betray his friends. October 20, 1997
- Favor the Bold (part five): As Rom is scheduled to be executed by Dukat, Sisko must convince Starfleet to mount an all-out assault to retake Deep Space 9. October 27, 1997
- Sacrifice of Angels (part six): Sisko leads a fleet of Federation ships to prevent the Dominion from disarming the wormhole minefield. November 3, 1997
- You Are Cordially Invited: With Deep Space 9 back in Federation hands, the time is ripe for a wedding between Worf and Jadzia. The only complication now is Martok's wife, whom Jadzia must appease if she is to marry Worf. November 10, 1997
- Resurrection: The Mirror Universe's Bareil arrives on the station, seeking sanctuary. November 17, 1997
- Statistical Probabilities: Bashir finds himself caring for an eccentric group of augmented humans, who all believe that the Federation's defeat at the hands of the Dominion is not just likely; it's inevitable. November 24, 1997
- The Magnificent Ferengi: The Dominion has kidnapped Quark's mother. Quark rounds up a posse of Ferengi to undertake a desperate rescue mission. January 1, 1998
- Waltz: Sisko and Dukat find themselves stranded on a hostile world, with Dukat's sanity deteriorating in the face of his manifold failures and the death of his daughter. January 8, 1998
- Who Mourns for Morn?: Morn has died and left a considerable estate of gold-pressed latinum to Quark. Unfortunately, others have come to collect on Morn's will. February 4, 1998
- Far Beyond the Stars: The Prophets give Sisko a vision that places him in the shoes of Benny Russel, a sci-fi writer struggling with racism in 1950s Harlem. February 11, 1998
- One Little Ship: A spatial anomaly has shrunken a runabout with Bashir, O'Brien, and Jadzia on it. They must find a way to regain their original size while also fighting off a group of Jem'Hadar boarding the Defiant. February 18, 1998
- Honor Among Thieves: O'Brien goes undercover to infiltrate a criminal organization colluding with the Dominion. February 25, 1998
- Change of Heart: Worf and Jadzia find themselves stranded on a distant planet, forcing Worf to decide: complete his mission, or save his wife. March 4, 1998
- Wrongs Darker Than Death or Night: Kira travels back into the past to witness the Cardassian occupation of Bajor, spurred by rumors that her mother was Dukat's lover. April 1, 1998
- Inquisition: Bashir is investigated by Starfleet for accusation of being a Dominion spy. April 8, 1998
- In the Pale Moonlight: Sisko must find a way to convince the Romulans to join the Federation and Klingons against the Dominion. April 15, 1998
- His Way: Odo meets Vic Fontaine, a holographic lounge singer, for advice on how to confess his love for Kira. April 22, 1998
- The Reckoning: An ancient tablet brings the eternal conflict between the Prophets and the Pah-wraiths to Deep Space 9. April 29, 1998
- Valiant: Jake and Nog are saved from Jem'Hadar soldiers by the Valiant, a ship whose crew consists only of young Starfleet cadets. May 6, 1998
- Profit and Lace: The Grand Nagus is ousted after the scandalous proposition of Ferengi suffrage, forcing Quark to go undercover as a Ferengi female to prevent his nemesis Brunt from taking the throne. May 13, 1998
- Time's Orphan: O'Brien's daughter Molly is involved in an accident with a time portal that causes her to return to the present time ten years older and feral from a lack of human contact. May 20, 1998
- The Sound of Her Voice: Sisko leads a mission to save a captain stranded on a hostile world as Quark attempts to conduct smuggling with Odo none the wiser. June 10, 1998
- Tears of the Prophets: Against the warnings of the Prophets, Sisko leads the invasion of Cardassia, only for his decisions to cost greatly. June 17, 1998
Season 7 (September 30, 1998 - June 2, 1999)
- Image in the Sand (part one): Sisko has resigned from leading Deep Space 9 and returned to Earth to work in his father's restaurant, only for images from a young woman to spur him back into action. September 30, 1998
- Shadows and Symbols (part two): Sisko attempts to get back into contact with the Prophets, while the Pah-Wraiths attempt to thwart him. October 7, 1998
- Afterimage: Ezri, the new host for the Dax symbiont, must find a way to work with her colleagues in the wake of Jadzia's untimely death. October 14, 1998
- Take Me Out to the Holosuite: Sisko decides to settle a rivalry with a pompous Vulcan captain the only way he knows how: with a rousing game of baseball. October 21, 1998
- Chrysalis: Bashir reunites with his Augment friends to help one of them recover after falling into a coma. October 28, 1998
- Treachery, Faith, and the Great River: Odo is contacted by Weyoun, one of the leaders of the Dominion, who expresses a desire to defect to the Federation. November 4, 1998
- Once More Unto the Breach: An old Klingon warrior, Kor, seeks to enter the fray against the Dominion. The only thing standing between him and glory, however, is Martok. November 11, 1998
- The Siege of AR-558: Sisko must command a battered Starfleet unit that has endured endless Jem'hadar assaults for five months on a desolate planet, all for a communication post they can't crack. November 18, 1998
- Covenant: Dukat, now working with the Pah-Wraiths, leads a cult of like-minded followers that Kira must dismantle. November 25, 1998
- It's Only a Paper Moon: Nog, struggling with injuries and mental trauma from the Dominion War, finds himself retreating into a holosuite fantasy to avoid facing the cruel nature of reality. December 30, 1998
- Prodigal Daughter: O'Brien has gone missing, and Ezri must enlist the aid of her mother in finding him. January 6, 1999
- The Emperor's New Cloak: The Grand Nagus has been abducted, and Quark and Rom must mount a rescue mission into the Mirror Universe. February 3, 1999
- Field of Fire: Ezri must call upon the memories of Joran, a serial murderer who was once a host for the Dax symbiont, to investigate a new spate of deaths. February 10, 1999
- Chimera: Odo meets another changeling, one of a small handful who had been sent out in times long past to explore the galaxy. February 17, 1999
- Badda-Bing, Badda-Bang: Holographic mobsters have taken over Vic Fontaine's holosuite casino, and Sisko and crew must help him take it back. February 24, 1999
- Inter Arma Enim Silent Leges: Bashir is thrust into a game of espionage as a secret cabal of Federation spies attempt to manipulate Romulus. March 3, 1999
- Penumbra (part one): As Sisko plans to marry Kasidy, Worf goes missing behind enemy lines, with Ezri mounting a rescue mission. April 7, 1999
- 'Til Death Do Us Part (part two): The Prophets warn Sisko not to go through with his wedding to Kasidy as Ezri and Worf are captured by the warlike Breen. Meanwhile, an unseen force is manipulating Kai Winn. April 14, 1999
- Strange Bedfellows (part three): Worf and Ezri's lives hang in the balance as the Breen and the Dominion join forces. Meanwhile, Kai Winn turns her back on the Prophets and sides with the Pah-Wraiths and their mysterious messenger. April 21, 1999
- The Changing Face of Evil (part four): As Kai Winn reads the forbidden texts of the Pah-Wraiths, the Dominion launches an invasion of Earth. April 28, 1999
- When It Rains... (part five): Sisko helps the Cardassians rebel against the Dominion as a plague ravages Odo and the changelings. May 5, 1999
- Tacking into the Wind (part six): The Klingons take the fight to the Breen. All the while, Kira attempts to steal a weapon the Breen are developing. May 12, 1999
- Extreme Measures (part seven): Bashir and O'Brien must infiltrate the mind of a Federation spy to save Odo from the disease ravaging him. May 19, 1999
- The Dogs of War (part eight): Kira is ambushed on Cardassia as Quark discovers he may become the next Grand Nagus. May 26, 1999
- What You Leave Behind (part nine): The Dominion War reaches its conclusion as Sisko fights to defeat Dukat and fulfill his destiny as the Bajoran Emissary. June 2, 1999