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Season SIX
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| Picture: | Episode: | Description: | Stardate: |
| A Time to Stand | Sisko and his crew are given an undercover mission that could change the balance of the Dominion war. |
Unknown | |
| Rocks and Shoals | Sisko and his beleaguered crew are captured by the Jem'Hadar. |
51107.2 | |
| Sons and Daughters | Worf is reunited with his estranged son, Alexander. | Unknown | |
| Behind the Lines | Various Deep Space Nine crewmembers must play a part in the battle with the Dominion. | 51149.5 | |
| Favor the Bold | The Federation continues to lose the war with the Dominion/Cardassian Alliance — and morale is sinking fast. |
Unknown | |
| Sacrifice of Angels | Dukat loses a daughter, while the Alpha Quadrant gains a victory. |
Unknown | |
| You Are Cordially Invited... | Worf's plans for a traditional Klingon wedding are threatened when Martok's wife refuses to accept Dax into their family. |
51247.5 | |
| Resurrection | When a stranger beams aboard the station and takes Kira hostage, she is shocked to see that he looks exactly like her dead love, Vedek Bareil. |
Unknown | |
| Statistical Probabilities | With the secret of his genetically-engineered past out in the open, Bashir is asked to work with a group of others like him. | Unknown | |
| The Magnificent Ferengi | The Grand Nagus calls with news that Quark's mother, Ishka, has been captured by the Dominion. |
Unknown | |
| Waltz | En route to Gul Dukat's war crimes investigation, Sisko meets with the former Cardassian leader, now a prisoner. | 51413.6 | |
| Who Mourns for Morn? | The crew is shocked to learn that Morn has been killed in an ion storm. | Unknown | |
| Far Beyond the Stars | After a friend's ship is destroyed and Sisko considers leaving Starfleet, he begins having visions of his crew as 1950s Americans. |
Unknown | |
| One Little Ship | In order to investigate a rare subspace phenomenon, Dax, O'Brien, and Bashir board the Runabout, U.S.S. Rubicon, that is shrunken to four inches long. | 51474.2 | |
| Honor Among Thieves | Starfleet Intelligence recruits Chief O'Brien to infiltrate the Orion Syndicate, the Alpha Quadrant's leading organized crime ring, to find a Starfleet informant. | Unknown | |
| Change of Heart | Worf must choose between Starfleet duty and his wife. |
51597.2 | |
| Wrongs Darker than Death or Night | Kira finds out some shocking news about her mother. |
Unknown | |
| Inquisition | Dr. Bashir is interrogated by a member of Section 31 — a branch of Starfleet Intelligence that answers to no one. | Unknown | |
| In the Pale Moonlight | Sisko goes to great lengths to enlist Romulan support in the Dominion war. |
51721.3 | |
| His Way | A new Holosuite program gives birth to "Vic," a 60's crooner who also provides advice for the lovelorn. |
Unknown | |
| The Reckoning | Sisko is called to Bajor when an ancient tablet addressing the Emissary is discovered. |
Unknown | |
| Valiant | Jake and Nog find themselves on board a rogue starship, piloted by a fresh-faced crew of Starfleet cadets. |
Unknown | |
| Profit and Lace | When Zek's status as the Ferengi Grand Nagus is in jeopardy following his revolutionary ideas about female rights, Quark temporarily changes sexes to prove a point. | Unknown | |
| Time's Orphan | While on a picnic, young Molly O'Brien disappears in a mysterious vortex, only to reapear as an 18-year-old woman. | Unknown | |
| The Sound of Her Voice | The Defiant unknowingly picks up a time-displaced distress call. |
Unknown | |
| Tears of the Prophets | A valued Deep Space Nine crewmember meets an untimely end. |
Unknown |