Now, to this day when Star Trek fans think of extended arcs they really have just one in mind, and that’s Deep Space Nine’s Dominion War arc.
The war itself doesn’t begin until the end of the fifth season, and I’ve broken it down to thirty-six key episodes (six of them consisting of two-part episodes with the same name, although the series features multiple two-part episodes with separate titles, including in the war arc). Since this one’s so long I won’t waste much time with preamble or dwell much on any one installment, instead a brief note on what it contributes to the arc.
At the end of the second season, “The Jem’Hadar” at last let’s us see the Dominion after many previous references to what dominates the other side of the wormhole introduced in the first episode, the Gamma Quadrant equivalent to the Federation. It ends with a big swerve when we learn that the Jem’Hadar are mere foot soldiers, and that they are controlled in part by the Vorta.
The third season begins with the two-part “The Search,” which serves the dual purpose of exploring the initial ramifications of contact with the Dominion as well as revealing the truth of shapeshifting Odo’s origins: he hails from the Founders. As in, Founders of the Dominion…
In “Improbable Cause”/“The Die Is Cast,” factions within the Romulan Star Empire and Cardassian Empire attempt an invasion of the Gamma Quadrant, and are met with a spectacular and definitive defeat.
The season ends with the further threat of Founder infiltration in “The Adversary.”
The fourth season begins by ramping up the threat in the two-part “Way of the Warrior,” in which the Dominion manipulates the Klingon Empire into war with the Cardassians.
In “Homefront”/“Paradise Lost,” the Founders infiltrate Earth and sow chaos within Starfleet itself.
In the fifth season premiere “Apocalypse Rising,” the true identity of the Founder infiltrator within the Klingon Empire is finally revealed.
Later, we meet the real Martok (the guise of the infiltrator dating back to “Way of the Warrior”) in a Dominion prison camp also hosting the remains of the Romulan/Cardassian fleet, as the Cardassians officially join the Dominion during “In Purgatory’s Shadow”/“By Inferno’s Light.”
Then, in “Call to Arms,” the season finale, the station is evacuated and the war begins.
The sixth season kicks off with the famous six-episode continuous arc, the first real extended serialization in franchise history: “A Time to Stand,” “Rocks and Shoals,” “Sons and Daughters,” “Behind the Lines,” “Favor the Bold,” and “Sacrifice of Angels,” which of course culminates in the retaking of the station.
The season continues to explore the war in a variety of ways from that point. “Statistical Probabilities” is a pessimistic view of its eventual outcome. “Waltz” sees the psychological fallout for Dukat. “In the Pale Moonlight” is probably the single best episode of the whole arc, in which Sisko grapples with his conscience.
Finally, in “Tears of the Prophets,” the biggest casualty of the war occurs: Jadzia Dax.
The seventh and final season continues and concludes the war. “The Siege of AR-558” is a straight-up war story, complete with a post-traumatic stress fallout follow-up, “It’s Only a Paper Moon.”
The final ten episodes of the series are a second grand serialization: “Penumbra,” “’Til Death Do Us Part,” “Strange Bedfellows,” “The Changing Face of Evil,” “When It Rains…,” “Tacking Into the Wind,” “Extreme Measures,” “The Dogs of War,” and the two-part finale, “What You Leave Behind.”