Exploration of the Gamma Quadrant took place without major incident for nearly one year. However, on a seemingly routine trade mission by the Ferengi, Quark first heard whispers of the Dominion, which apparently was a union of civilizations similar to the Federation in its goals of mutual defense and trade practices. Quark, under the aegis of Grand Nagus Zek, was authorized to negotiate a trade agreement with the Dominion; these negotiations were ultimately successful.

However, as races from the Alpha Quadrant began to colonize planets in the Gamma Quadrant and make their presence known to Gamma Quadrant species, disturbing reports about the Dominion began to emerge. The reports seemed to indicate that what the Dominion could not attain through trade would be taken by force. These reports were borne out in 2370 when a huge fleet of Skrreean ships appeared in the Alpha Quadrant, in search of a new homeworld after their old home had been utterly destroyed by Dominion forces.



Toward the end of 2370, Sisko, his son Jake, Quark, and Quark’s nephew Nog were visiting an uninhabited Gamma Quadrant planet to do a planetary survey for a school project of Jake’s and Nog’s. It was here that the Jem’Hadar—the Dominion’s military forces—were first encountered, and Sisko and Quark were captured by these forces, along with a mysterious alien (later to be identified as a Vorta) named Eris. The Jem’Hadar then sent a representative to DS9 to inform the Alpha Quadrant that no further intrusions into Dominion space would be tolerated, and gave Major Kira Nerys a list of colonies and starships already destroyed for trespassing.
The U.F.P. responded by sending a rescue team consisting of the ''Galaxy''-class starship ''Odyssey'' and all three of DS9’s runabouts. They managed to pull off the rescue (Eris included); however, a fierce battle ensued with three Jem’Hadar attack ships. One of the Jem’Hadar attack ships made a kamikaze run for Odyssey’s warp core, using its phased polaron beam to punch through her shields despite rotating shield harmonics.
At the time of her destruction, the Odyssey had already sustained casualties on decks 4, 5, 8 and 17, a plasma leak in the port nacelle, major damage to Deck 7, and the loss of phaser power, external communications, and weapons control. The remaining forces returned to the Alpha Quadrant, where it was discovered that Eris was a spy and that Sisko’s capture had been engineered by the Founders, the shadowy ruling class of the Dominion. Once discovered, Eris managed to escape DS9 using some sort of a transporter technology, seemingly far more advanced than Alpha Quadrant species had been able to develop. (Episode: “The Jem’Hadar”)

Cardassian and Dominion forces launched their attack on Deep Space Nine to wrest control of the station from the Federation. In a calculated strategic move, U.F.P. and Klingon forces were at the time attacking the Dominion shipyards at Torros III, leading to the loss of DS9. However under advice from Captain Sisko, the Bajoran government had signed a treaty of non-aggression with the Dominion, and this allowed Bajoran forces to remain on the station and Bajor untouched by the Dominion/Cardasian allience. Further, Major Kira Nerys activated a computer program that completly disabled DS9's computer systems, rendering the station effectivly useless over the short/medium term, under the assumption that Starfleet would quickly retake the station before it could be restored to operational status. This esimate of a short occupation proved to be highly optimistic. (Episode: “Call to Arms”) In 2374, while Gul Dukat and Weyoun were trying to figure out a way to safely dismantle the minefield, Kira began her own resistance movement on the station, sowing discord between the Cardassians and Jem’Hadar on the station, particularly between Dukat’s second-in-command—Gul Damar—and Dominion forces. (episode: “Behind the Lines”)



By the late spring of 2374, it was clear the Federation and the Klingon Empire were slowly losing the war despite their blockade. Several Dominion strategic advantages such as extreme range sensor arrays that monitored Federaiton fleet movements and let the Dominion concentrate forces against them proved highly damaging in the early months of the war. As Miles O'Brien put it, "Engage-Retreat" was becoming the tune the Federation and Klingon fleets were dancing to. Therefore, Sisko convinced the top brass in Starfleet that the key strategic point of the conflict would not be any one planet, but rather Deep Space Nine itself. In what was dubbed Operation Return, a fleet made up of elements from 3 Federation commands would be put together, with involvement of the Klingon Defense Forces to retake the Station and swing momentum back to the Alliance.

However, information was passed through the lines that indicated Dukat was very close to dismantling the minefield. Despite the fact that elements of the Federation task force had not yet arrived, nor had the Klingons, the decision was made to launch with what they had. (Episode: “Favor the Bold”) With nothing left to lose, the Federation launched its assault (known as the Battle of Bajor) with 600 ships against 1254 Dominion ships, and with timely intervention by the Klingons, the Defiant was able to break through Dominion lines and make it to the wormhole just as the minefield was taken down, despite the best efforts of Major Kira, Odo and several Bajoran security officers on DS9. In a desperate and futile attempt to delay the thousands of Dominion ships pouring through from the Gamma Quadrent, Sisko entered the wormhole, at which point the Prophets decided to intervene. Apparently, Sisko had not yet completed his tasks as the Emissary to the Bajorans. Foreseeing that he would die in his valiant attempt to stop the Dominion forces from coming through, the Prophets stepped in. It is unknown exactly what happened to the Dominion fleet while it was traversing the wormhole; the fleet is (in the words of Miles O’Brien) “just gone”—it simply disappeared. With Cardassian morale broken, and with 200 Allied ships having broken through the lines of their fleet and headed directly to the station, they abandoned Ter'ak Nor, and the U.F.P. once again took control of Deep Space Nine. The Federation victory by Deus ex machina cost Dukat his sanity, and Damar was put in his place as the Cardassian head of state, though he was much more a Dominion puppet than Dukat. (Episode: “Sacrifice of Angels”)

With the Dominion having pulled back mostly to Cardasian space, it appeared that the Dominion war could have been over. Indeed Damar and Weyoun arrived at DS9 shortly afterwards to negotiate a peace treaty with the Federation-Klingon Alliance raising hopes for an end to the war. In actual fact, it was an attempt to gain control of a key planet with which a secure Alpha Quadrant supply of Ketracel white could be obtained. The Federation nonetheless supported the treaty as according to a strategic study by Doctor Bashier, the Dominion would be forced to attack instantly before their stockpiles ran out, if they could not secure a supply.

For a time the war simmered down to a low level conflict as both sides licked their wounds.

Unfortunantly, it turned out Jem'Hadar breeding technology combined with advanced Dominion shipyard mass production meant the Dominion recovered first.

After half a year of relative peace with relativly minor border skirmishes (including Jem'Hadar ships running through Romulan space, crossing the Neutral zone and attacking the Federation before retrating thanks to their non-aggression treaty), the war turns hot once again. The Dominion, taking advantage of a Federation fleet moving out of position (though evidence suggests they knew it was going to happen well in advance) to conduct exercises, invades and capture Betazed in a textbook surprise attack, giving them a forward base to raid deep into the Federation.

Sisko, convinced that the Romulans are critical to changing the strategic situation enough to allow the Alliance to go on the offensive (and with the backing of Starfleet Command) schemes with Garak (the only Cardassian with permanent residence on DS9 and a former master spy for the Obsidian Order)—to plant false evidence of a Dominion plot to invade Romulus, the Romulan homeworld and capital planet of the Romulan Star Empire. The Romulan Senator Vreenak was shown the “evidence” and despite the best efforts of the conspiracy, discovered it was in fact a forgery. Furious, Vreenak planned to return to Romulus to reveal the plot to the entire Alpha Quadrant, an act which would have destroyed any chance of an alliance with the Romulans and perhaps even motivated them to form an alliance with the Dominion.

However, the Senator’s shuttle mysteriously exploded during its return trip and the blame was pointed at the Dominion. Sisko confronted Garak, who revealed that he had placed a bomb on board, because the evidence of a Dominion plot against the Romulans would seem like the perfect motive to murder the Senator (the evidence "miracously" surviving the explosion and after several days of painstaking rebuilding, presenting the evidence Sisko and Garak had fabricated...with any imperfections being therefore attributed to the explosion. Garak explains his actions:

Garak
"So, with a seemingly legitimate data-rod in one hand and a dead senator in the other, I ask you captain, what conclusion would you draw?

Sisko.
"That Vreenak obtained the rod on Soukara and that the Dominion killed him to prevent him from returning to Romulus with it.

Garak:
"Precisely. And the more the Dominion protests their innocence, the more the Romulans will believe they're guilty... because it's exactly what the Romulans would've done in their place!"

A few days later, the Romulan Star Empire formally decalared war against the Dominion, swinging the Strategic balance firmly in favour of the Alliance.

Around the same time of the formation of the alliance with the Romulans, DS9’s chief medical officer, Dr. Julian Bashir, was made aware of the existence of Section 31—a covert intelligence (and "officially" unsanctioned) agency similar to the Obisidian Order—within the Federation. Section 31 seemed intensely interested in manipulating the war behind the scenes and tried to recruit Bashir into their ranks. Bashir refused, informed Sisko of Section 31’s existence, and adopted a “wait-and-see” attitude. (episode: “Inquisition”)



With the Romulan fleets now helping to replace the losses the Alliance had taken early in the war, the Alliance now moved onto the offensive, for the first time invading true Cardassian space and taking the strategic Chin’toka system from the Dominion in early 2375.

Section 31 had also been busy, but far earlier then anyone anticipated: they had infected Odo with a virus that he unknowingly communicated to the rest of the Founders by linking the Great Link many years before the war started. Section 31 had seen the Dominion as a clear Strategic Threat to the Alpha Quadrent and Federation and had taken action, much as the Tal'Shiar and Obsidian order had, but far more subtly and successfully. For as the Founders died, so did the Dominion.

The disease began to take its toll on the Founders in mid-2375, seriously damaging their ability to change shape and the female founders ability to lead the war effort. (Episode: “Treachery, Faith, and the Great River”) Legate Damar, too, grew increasingly frustrated with the seemingly stalemated war (Alliance momentum into Cardasian space had fallen after Chintaka in the face of fanatic Dominion resistance) and his own position as a Dominion puppet. As Cardassian military losses mounted, he began to drink heavily and often criticized the Dominion’s ability to orchestrate the war successfully.

As the Dominion’s position became increasingly precarious with the Alliance continuing to gain the initiative, the female Changeling sought and successfuly formed an alliance with the Breen, a relatively unknown spacefaring species from the Alpha Quadrant. Their entry into the struggle temporarily turned the tide of the war back to the Dominion’s favor. (Episode: “’Til Death Do Us Part”) Breen vessels were equipped with a power-draining weapon that rendered any vessel it targeted completely inert. One Klingon vessel was unaffected thanks to a slight modification to its engine core. The rest of the Klingon fleet made these alterations in order to fight the Breen and Dominion. However this left the by now (after the war with Cardasia, the Federation and Dominion) heavily diminshed Klingon fleet outnumbered close to 20-1, allowing the Dominion to stabilize its front lines and retake the Chin’toka system in a battle that destroyed the USS Defiant (among others). Breen forces also staged a sneak attack on Earth itself, destroying many Starfleet facilities as well as heavily damaging the Golden Gate Bridge in San Francisco. While a tactical defeat (the Breen forces were blasted by Starfleet and the damage was actually relativly minor), the strategic shockwaves of such a brazen act horrified many and proved that the Breen could strike fear in their enemy. (Episode: “The Changing Face of Evil”)

The Klingons, now alone at the front, were instructed by Alliance commanders to hold their position while Alliance scientists tried to figure how to counter the Breen’s energy-draining weapon. General Martoks strategy was to send battle groups in under cloak to conduct a rapid series of harrasement raids against soft targets, keeping the Dominion off balance and unable to muster an offensive, hopefuly for long enough for the Federation and Klingon fleets to come back on line. Unfortunatly, Klingon Politics came in the way. Klingon Chancellor Gowron began to fear that Martok’s military prowess and more criticaly, the loyalty of the KDF to Martok, would eclipse his own. He stripped command of the war from Martok and assumed leadership himself while placing Martok in no-win battles, wasting huge amounts of ships and men by throwing them against impossible targets, throwing the Alliance’s tenuous position into chaos. The situation reached a head when DS9’s strategic operations officer, Lieutenant Commander Worf, challenged Gowron’s leadership in open council. As per Klingon tradition, this meant a duel to the death between the two. Worf killed Gowron in this fight, and the remaining council leaders crowned Worf the new Chancellor of the Klingon Empire. Worf, however, refused this honor, giving it instead to Martok. With the Klingon political landscape somewhat stabilized after years of questionable management by Gowron (at least as far as The Dominion War was concerned), the war returned to near-stalemated conditions. (episodes: “When It Rains…” and “Tacking Into the Wind”)