A Man Alone Stardate 46421.5: Feeling on the station runs high when Odo is the main suspect in the murder of Ibudan, a Bajoran member of the underworld who Odo sentenced to jail during the Cardassian occupation. As a restless mob of the station’s denizens gather to confront Odo, Bashir makes the startling discovery that the murder victim is in fact a clone, created and subsequently murdered by the real Ibudan in order to implicate Odo. In a final twist of irony, Ibudan is swiftly apprehended by Odo, and is accordingly charged with the murder of his own clone. Meanwhile, after Jake and his new Ferengi friend, Nog, are caught playing pranks on the promenade, and in an effort to overcome her own feelings of inadequacy, Keiko O’Brien decides to open a school on the station.

Babel Stardate 46423.7: In the midst of being inundated by a spate of maintenance requests, O’Brien inadvertently triggers a dormant Bajoran booby trap left over from the Occupation that spreads a lethal virus through the station’s food replicators, and causes an advanced form of aphasia. As the virus rapidly mutates into an airborne strain, all of the station’s officers gradually become incapacitated and the fate of the station is left to Odo and Quark who avert a dangerous situation when a panicky alien attempts to flee the station. With the station placed under quarantine, and in a desperate attempt to find a cure, Kira travels to Bajor and kidnaps the co-creator of the virus by beaming him into her runabout, and is forced to extort the unwilling scientist by exposing him to the virus in an effort to gain his assistance.

Captive Pursuit Stardate not given: The station receives its first visitor from the Gamma Quadrant, an unannounced ship carrying a single lifeform named Tosk, who happened to spot another ship going through the wormhole and followed it. The visitor's starship is damaged and requires help from the station. While awaiting repairs the visitor is followed by another starship from the Gamma Quadrant, which promptly scans the station and comes after Tosk, who by this time is cooling his heels in one of Odo's security chambers. The crew of the new ship, transport over and attempt to take Tosk forcibly. After a battle with station security the leader locates Tosk, captive of DS9 security. Further negotiations calm the situation down; we find Tosk is the "hunted" while the others are the "hunters", all players in a deadly game of galactic hide-and-seek.

Q-Less Stardate 46531.2: The runabout Ganges returns to the station with hardly any power and its crew and passengers in danger from lack of life support. Jadzia Dax and another crewman have returned with Vash after finding her in the Gamma Quadrant. With her is Q who is hounding Vash as a traveling companion, trying to get her to accept him. Also along are several artifacts which Vash has acquired during her travels. She makes fast friends with Quark and strikes up a bargain with the Ferengi profiteer to auction them off, but there's a danger posed by one of the items, an embryonic lifeform imprisoned inside a huge, glowing gem, which Q obviously knows but doesn't let on, in his familiar position of being the only one who knows the cards on the table.

Dax Stardate 46910.1: After sharing a drink with Dr. Bashir, Dax is accosted by a group of men on her way back to her quarters, intent on taking her by force back to Klaestron IV to stand trial for treason and the murder of General Ardelon Tandro. The attempt falls short and DS9 becomes the site of an extradition hearing, which allows the story to delve into the rights of the Trill host Jadzia Dax, and her former joined host, Curzon Dax who is actually the accused. But in the course of the hearing it turns out that not Curzon Dax but the late General Tandro himself betrayed his army to the rebel faction on Klaestron. 

The Passenger Stardate not given: Major Kira and Dr. Bashir are aboard the Rio Grande when they respond to a distress signal sent by another ship. While Kira puts out fires, Bashir tends to the remaining lifesigns reviving first a female security official and the other, her prisoner. After applying a hypospray, the prisoner assaults Bashir briefly then dies. Kira, Bashir and the female beam back to the runabout with the body of the prisoner, heading back to DS9 with the damaged ship in-tow. The prisoner turns out to be an arch-villain and after several twists and turns almost succeeds at commandeering a starship arriving from the Gamma Quadrant filled with rare deuridium, for his own nefarious purposes.

Move Along Home Stardate not given: A Vulcan ship has made contact with a new species in the Gamma Quadrant and Sisko and his senior officers don their dress uniforms to greet them when the arrive at DS9. Highly interested in games, the newcomers gamble at Quark's where they catch the Ferengi cheating. As a penalty, Sisko and his senior officers are trapped inside a game world controlled by the Wadi, while Quark and Odo watch helplessly, reacting to the game as they go, in an attempt to free their comrades. When Quark thinks that the officers are lost because of his fault, the Wadi leader declares that it was all just a game.

The Nagus Stardate not given: DS9 is invaded by the Ferengi, come to hold a business conference at Quark's to discuss their future in developing the virgin Gamma Quadrant. Grand Nagus Zek feels that he is too old to lead and names Quark to take his place as Nagus, who accepts and shortly learns of the title's pitfalls and benefits. Zek's son Krax allies himself with Quark's brother Rom to assassinate the new Nagus. But Odo and Zek, who feigned his death, thwart the plan. Zek, now knowing that Krax is no worthy successor, decides to exploit the business opportunities in the Gamma Quadrant himself.

Vortex Stardate not given: A Miradorn raider docks at DS9, bringing plunder to sell behind the scenes at Quark's. The transaction is interrupted by an alien from the Gamma Quadrant who tries to steal an item but ends up killing one of the two Miradorn. Odo, after capturing him, finds out that the alien named Croden is wanted on his homeworld for previous crimes, but also discovers the man knows something about Changelings. During transport to Croden's homeworld the Miradorn's twin brother comes after the pair. They land on an asteroid, evade their pursuer and, after discovering that Croden was just going to take care about his daughter in stasis, Odo lets the wanted man go.

Battle Lines Stardate not given: DS9 receives a visit from Kai Opaka, the spiritual leader of Bajor, whom Sisko offered a tour of the station. Sisko also takes her and members  of his senior staff through the wormhole, where they find trouble. The runabout is attacked and it crash-lands on a moon, killing Opaka and leading the survivors into a strange netherworld where the dead seem to rise and live, and die, and live, and die... The asteroid is a penal colony where microbes keep the prisoners alive, causing them to wage an eternal war. Kai Opaka too is revived by the microbes. As she can't survive in the outside world she decides to stay behind and attempt to mediate.

The Storyteller Stardate 46729.1: While the station is hosting a diplomatic conference, Dr. Bashir and Chief O'Brien are sent to Bajor for a medical emergency. The two discover that an energy form of some type periodically attacks the village, and does so while the pair are there. Aiding the dying sirah, a "storyteller", O'Brien helps back away the strange phenomenon the locals call "Dal'Rok". After saving the village the locals proclaim O'Brien as their new sirah, angering Hovath, the old sirah's apprentice. The Dal'Rok is in reality a manifestation of the village's anger and can be defeated only with unanimity. When O'Brien fails during another attack of the Dal'Rok, the young Hovath, who was always meant to be the successor but lacked the necessary determination so far, successfully takes over the task.

Progress Stardate 46844.3: The station is assisting the Bajoran government in an energy transfer, tapping the molten core of Bajor's fifth moon in an attempt to provide energy for the main world. The moon holds some settlers and Kira and Dax are dispatched with a runabout to make sure the evacuation is complete before the transfer can begin. Sensors pick up lifeforms and Kira beams down to find a group of Bajoran farmers who refuse to leave their home. After spending some time with an old man named Mullibok with whom she sympathizes Kira eventually decides that there is no way back and destroys his house.

If Wishes Were Horses Stardate 46853.2: Various manifestations of the crew's imagination come to life and threaten the station, such as Buck Bokai, a 21st century baseball player, Rumplestiltskin, a fairy-tale character, a sensual version of Dax that so far existed only in Bashir's mind and other strange effects. Everything is actually the result of a new race making first contact with the Federation, without their knowledge.

The Forsaken Stardate 46925.1: A group of Federation ambassadors arrive on the station, proceeding with a fact-finding mission concerning the wormhole. A pompous and demanding group, Sisko has the foresight to assign Dr. Bashir to escort them about the station while he tends to business. Among the ambassadors is Lwaxana Troi who develops an interest for Odo. Shortly afterwards a probe comes through the wormhole and the station begins to experience strange technical difficulties. O'Brien manages to contain the alien program which he thinks of as a "pup" in what he calls a "doghouse".

Dramatis Personae Stardate 46922.3: A Klingon ship explodes just after exiting from the wormhole. The vessel's first officer is able to beam aboard the station, but dies after cryptically uttering the phrase "Victory!". In addition, a Valerian ship has put into port and Kira suspects they are dealing with Cardassia as they did during the occupation. She and Sisko butt heads initially, as the Federation has no reason to challenge the Valerian's purpose. Slowly, cracks develop between the various factions and alliances of the station staff, escalating and dividing the station into several opposing camps each scheming to eliminate the other. Odo and Quark manage to remove the cause for the tensions, the Saltah'na energy spheres which were responsible for the destruction of the Klingon vessel as well.

Duet Stardate not given: A freighter docking at the station requests medical help for a passenger it is transporting. The passenger turns out to be a Cardassian with a case of Kalla-Nohra syndrome, a rare disease obtainable only from those who were located at labor camps during the Bajoran occupation. Kira Nerys has the man placed under arrest and delves into his background. The man then admits to be Gul Darhe'el, the notorious commandant of the labor camp at Gallitep. But it turns out that he is actually just a low-ranking executive named Marritza. By posing as one of the biggest war criminals in Bajoran history he wanted to make the case public and help alleviate Cardassia's and his own guilt. When Marritza is released and about to return to his home planet, a Bajoran appears from the crowd and stabs him - apparently just because Marritza is a Cardassian.

In the Hands of the Prophets Stardate not given: Keiko O'Brien is conducting class when Vedek Winn shows up and confronts her about her non-religious teachings. Using this as platform she then foments fervor against the Federation and Commander Sisko in particular. Tensions rise on the station, culminating in an attempted assassination by Neela, a member of Chief O'Brien's staff, who is foiled in the last moment. While Winn's involvement in the scheme remains obvious yet unproven, the events bring the Bajorans and the Federation closer together rather than driving them apart.

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