- 1 Apocalypse Rising
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Stardate: Unknown Gowron is suspected of being replaced by a changeling. Sisko, Odo and O'Brien go undercover as Klingons, only to discover the real infiltrator is General Martok.
Air Date: 1996-09-30
- 2 The Ship
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Stardate:50049.3 While searching for minerals on a planet, Sisko, Dax, O'Brien, Worf, and Muniz discover the wreckage of a crashed Jem'Hadar ship. However, they are not the only ones interested, because the Dominion is anxious to retrieve the vessel.
Air Date: 1996-10-07
- 3 Looking for par'Mach in All the Wrong Places
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Stardate: Unknown Worf falls in love with Quark's ex-wife, Grilka. However, Quark is also still interested.
Air Date: 1996-10-14
- 4 ...Nor the Battle to the Strong
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Stardate: Unknown Jake Sisko and Julian Bashir are caught in the middle of a battle between a Federation colony and a Klingon army.
Air Date: 1996-10-21
- 5 The Assignment
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Stardate: Unknown A Pah'wraith (evil entities who are enemies of the Bajoran Prophets) possesses and impersonates Keiko, but reveals her identity to Miles, threatening to kill her if he doesn't carry out her mysterious instructions.
Air Date: 1996-10-28
- 6 Trials and Tribble-ations
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Stardate:4523.7 While returning to Deep Space Nine with the Bajoran Orb of Time, the crew are thrown back to the 23rd Century. They must infiltrate the original Starship Enterprise in order to stop an undercover Klingon from poisoning a shipment of grain being carried.
Air Date: 1996-11-04
- 7 Let He Who is Without Sin...
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Stardate: Unknown Worf, Dax, Leeta, Quark and Bashir pay a visit to Risa. Things go bad when a band of rebels gains control of the planet's weather regulator to scare the visitors in an attempt to show them how unprepared the Federation is for the Dominion invasion.
Air Date: 1996-11-11
- 8 Things Past
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Stardate: Unknown Sisko, Odo, Dax and Garak are shifted into the past, when DS9 was known as Terok Nor. To each other, they appear normal, but to others they appear as Bajoran slaves. Soon they are accused of planting a bomb, and are sentenced to death.
Air Date: 1996-11-18
- 9 The Ascent
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Stardate: Unknown Odo and Quark are stranded when they crash on a planet with no communications or replicators. Their only hope to be found is if they can climb to the top of a high mountain. Back on the station, Jake and Nog are moving in together. However, it doesn't go as smoothly as they thought.
Air Date: 1996-11-25
- 10 Rapture
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Stardate: Unknown Sisko discovers the legendary Bajoran city of B'hala. He also receives visions of Bajor's future, one of which warns him not to let Bajor join the Federation.
Air Date: 1996-12-30
- 11 The Darkness and the Light
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Stardate: 50416.2 One by one, members of the Shakaar resistance cell are murdered, and Kira becomes increasingly worried that she will be next.
Air Date: 1997-01-06
- 12 The Begotten
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Stardate: Unknown Kira goes into labor with Keiko's child. Odo buys an infant changeling from Quark that was found drifting in space. Tensions rise when the scientist that first studied Odo, Dr. Mora Pol, arrives to give Odo a helping hand.
Air Date: 1997-01-27
- 13 For the Uniform
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Stardate: 50485.2 Sisko encounters Eddington, his former security chief turned Maquis traitor, and he is more desperate to capture him than ever.
Air Date: 1997-02-03
- 14 In Purgatory's Shadow (1)
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Stardate: Unknown After a coded Cardassian message from the Gamma Quadrant is detected, Garak and Worf attempt a rescue. However, they are captured by the Jem'Hadar and imprisoned in the same cell as Enabran Tain, General Martok, and the real Julian Bashir, who had been secretly replaced several weeks prior without any notice. The Jem'hadar fleet invades the Alpha Quadrant when an attempt to seal the wormhole is sabotaged by the changeling-Bashir.
Air Date: 1997-02-10
- 15 By Inferno's Light (2)
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Stardate: 50564.2 When the Dominion fleet comes through the wormhole, it soon becomes clear that Cardassia has allied itself with the Dominion and that war is not far off. As the forces of the Alpha Quadrant assemble, the changeling posing as Dr. Bashir is wrecking havoc on Deep Space Nine.
Air Date: 1997-02-17
- 16 Doctor Bashir, I Presume?
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Stardate: Unknown Bashir is chosen as the model for Starfleet's next Emergency Medical Holographic Doctor. During the process it is revealed that Julian was illegally genetically enhanced as a child, rendering him a genius. However, his father must now face a jail term or his son Julian will be court-martialled from Starfleet.
Air Date: 1997-02-24
- 17 A Simple Investigation
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Stardate: Unknown A woman has her memories erased and stored on a data crystal to infiltrate the Orion Syndicate. Odo falls in love with her, but must save her life by finding her data crystal.
Air Date: 1997-03-31
- 18 Business as Usual
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Stardate: Unknown Quark enters into the booming business of arms dealing with his cousin. However, his new enterprise may cost him his life.
Air Date: 1997-04-07
- 19 Ties of Blood and Water
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Stardate: 50712.5 A Cardassian dissident opposed to the Cardassian/Dominion alliance asks Kira to pose as his daughter so that he may reveal his secrets to use against his enemies as is customary in his culture. Kira must overcome painful memories of her own father's death before she can face him and gain the information.
Air Date: 1997-04-14
- 20 Ferengi Love Songs
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Stardate: Unknown Quark discovers that his mother, Ishka, is having a love affair with the Grand Nagus Zek. Back on the station, Leeta and Rom decide to get married. However, problems soon arise.
Air Date: 1997-04-21
- 21 Soldiers of the Empire
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Stardate: Unknown Worf and Dax join a Klingon ship captained by General Martok on his first mission since being freed from the Dominion prison. However, the crew is in such a low state of morale that when they encounter a Jem'Hadar warship, they enter a battle for their lives.
Air Date: 1997-04-28
- 22 Children of Time
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Stardate: 50814.2 The Defiant enters a barrier surrounding a planet in the Gamma Quadrant, only to find its inhabitants are the crew's descendants from 200 years in the past.
Air Date: 1997-05-05
- 23 Blaze of Glory
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Stardate: Unknown Sisko receives a message from one of the few surviving Maquis members saying that they will launch undetectable missiles at the Cardassians, which will provoke an all out war. Sisko enlists the help of Eddington to aid him in deactivating them, however, all is not as Sisko had been informed.
Air Date: 1997-05-12
- 24 Empok Nor
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Stardate: Unknown In order to repair the damaged Deep Space Nine, O'Brien assembles a team to salvage parts from the disbanded Empok Nor. However, their presence sets off an old booby trap that put all their lives in danger.
Air Date: 1997-05-19
- 25 In the Cards
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Stardate: Unknown Jake and Nog attempt to obtain an ancient baseball card to help lift Ben out of his depression. However, in order to get it from its new owner, they must steal equipment from the station, but this brings them under interrogation from the Dominion.
Air Date: 1997-06-09
- 26 Call to Arms (1)
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Stardate: Unknown Leeta and Rom get married. Sisko decides to mine the wormhole, which will likely start the war. When their plan is detected, Sisko is forced to evacuate the station and endorse the non-aggression pact between Bajor and the Dominion. While patrolling the border, General Martok detects the first wave of Dominion ships headed for Deep Space Nine. All remaining Starfleet personnel are ordered to leave the station. Kira, Odo, Quark, Rom, Morn and Jake stay behind on the station and disable it as it is handed over to the Dominion.
Air Date: 1997-06-16