The Star Trek Project
In 2369 the Cardassian occupation of the planet Bajor ended, the Cardassians having been driven off by various Bajoran resistance factions. These factions then formed a provisional government to oversee the rebuilding of the planet, which had been ecologically, culturally, and financially devastated by the occupation. One of its first official acts was to ask The United Federation of Planets for assistance in this monumental task.
The UFP responded by sending Commander Benjamin Sisko to take command of the space station Terok Nor, an orbital ore processing facility left behind by the Cardassians. This station was re-christened Deep Space Nine, and was to become a diplomatic and commercial center for Bajor. Sisko was tasked by Captain Jean-Luc Picard to do everything, short of violating the Federation's Prime Directive, to ensure that Bajor rebuilt itself enough to win entry into the Federation.
However, not long after the UFP's arrival, Sisko, along with science officer Jadzia Dax discovered a stable wormhole connecting Bajoran territory to the Gamma Quadrant of the Milky Way galaxy, nearly 70,000 light years away, a distance unattainable by any sentient race extant using conventional means. In order to protect Bajoran interests the station was moved from the orbit of Bajor to a point close to the Alpha Quadrant terminus of the wormhole. It was also discovered that the wormhole is actually home to aliens known to the Bajorans as The Prophets ... beings which exist in only one point in space (the wormhole) but all points in time, giving them a very non-linear view of the universe, where effect can precede cause. They, for unrevealed reasons, adopted Sisko as their emissary to the Bajoran people. Sisko didn't like this iconic role, especially since he was treated with religious reverence by the Bajoran people, but eventually learned to accept it, and use it from time to time to further the Federation's goal of helping Bajor to rebuild.
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 which was 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 and Nog's. It was here that the Jem'Hadar, the Dominion's elite military forces were 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 UFP responded by sending a rescue team consisting of the USS Odyssey, a Galaxy class starship, and all three of DS9's runabout class ships. They managed to pull off the rescue (Eris included), but got into a fierce battle with Jem'Hadar ships, and the Odyssey was destroyed, along with all crew aboard (non-essential personnel had, thankfully, been offloaded to DS9 before the mission) when a Jem'Hadar ship made a kamikaze attack upon it. The remaining forces returned to the Alpha Quadrant, where it was discovered Eris was a spy, and Sisko's capture engineered by the Founders, the shadowy ruling class of The Dominion. Once discovered, Eris managed to escape DS9 using transporter technology seemingly far more advanced than Alpha Quadrant species had been able to develop.
Early in 2371 Sisko returned to Earth for a Starfleet debriefing on the matter, returning to the space station commanding the USS Defiant, a prototype battle cruiser originally developed to fight the Borg, but modified with a Romulan cloaking device to enter the Gamma Quadrant on a peace mission to locate the Founders.
And find the Founders they do, discovering that they are the same race as Odo, DS9's shapeshifting chief of security. Despite a strong longing to return to his home, he finds his people's philosophy--that what you can control cannot hurt you--abhorrent. After a short standoff between Federation and Dominion forces, Odo asks to be returned to the Alpha Quadrant with all Federation forces intact. The Founders, led by the female shapeshifter, acquiese to Odo's request, in the hopes that Odo will one day rejoin his people. This marks the beginning of a Cold War phase between the Federation and Dominion, with limited skirmishes between the two sides, and a steady buildup of military forces.
Meanwhile, the other Alpha Quadrant powers were not sitting still in the face of the threat from The Dominion. The Obsidian Order, a covert Cardassian intelligence force led by Enabran Tain, allied themselves with the Tal Shiar, the Romulan equivalent of the Order. Together, they secretly built a huge fleet of starships in the Orrias sector of Cardassian space, and launched a preemptive strike against the Founders homeworld, hoping that the Dominion would collapse with the loss of the Founders.
However, the Founders, using their shapeshifting abilities, had infiltrated both groups and actually encouraged the strike, the better to launch a surprise attack and in one stroke, wipe out both the Order and the Tal Shiar. The Dominion stunned the galaxy with this plan, leaving only the UFP and the Klingon Empire as the remaining powers strong enough to stand up to the Dominion.
Late in 2371, it was learned that the Founders had infiltrated nearly every major power in the Alpha Quadrant, and the ensuring paranoia about who might or might not be a shapeshifter led to the Klingon invasion of Cardassian territory in 2372. With the fall of the Obsidian Order, the Cardassian citizenry had legitimately overthrown the militaristic government, putting a civilian based government in place. However, the Klingons didn't accept the sudden change in government, and suspected Dominion involvement. Their refusal to break off their invasion, even after it had been proven that the Dominion was not involved, led newly-promoted Captain Sisko to a military confrontation with the Klingons, as the Klingons, under Chancellor Gowron and General Martok attempted to seize DS9. The attack was repulsed--barely--but caused the Klingons to sever all diplomatic relations with the Federation, and to withdraw from the Khitomer accords, essentially ending decades of peace between the UFP and the Klingon Empire. This seemed to further the Founders goal of destabilization of the Alpha Quadrant as a prelude to their own invasion.
The paranoia over shapeshifters continued throughout 2372, and Starfleet responded by trying to implement a coup d'etat of the Federation after it was learned that shapeshifters had infiltrated Earth. This led to armed conflict between Starfleet vessels for the first time--since Khan Noonian Singh hijacked the USS Reliant--when Defiant and the USS Lakota exchanged fire. In the nick of time, Sisko was able to force Admiral Leyton to abandon his efforts to impose martial law on the Federation by convincing him to step down and face criminal charges.
Tensions between the UFP and the Klingon Empire continued to rise, and war broke out between the two in late 2372 over the Federation's refusal to recognize the Klingon's claim to the Archanis sector. However, the Empire could not effectively fight a war on two fronts, as the Cardassians, in mid-2373 and under the leadership of Gul Dukat (the former prefect of Terok Nor), officially became a member state of The Dominion. This gave the Founders a solid foothold in the Alpha Quadrant, and the Cardassians, who were nearly wiped out by the Klingon invasion, were able to drive the Klingons out of Cardassian space, inflicting heavy losses upon Klingon forces in doing so. With The Dominion now firmly entrenched in the Alpha Quadrant, the Klingon Empire re-affirmed the Khitomer Accords, ending the brief war between the Empire and the UFP.
The Dominion now began sending massive fleets of ships through the wormhole to bolster their presence in the Alpha Quadrant, and to reinforce Cardassian positions. The Federation and Klingon Empire decided that this was an untenable situation, and built a field of space mines at the mouth of the wormhole on the Alpha Quadrant side that were self-replicating and fitted with Klingon cloaking devices. This effectively cut off the Dominion's supply lines to the Alpha Quadrant. However, Gul Dukat and his Dominion advisor, the Vorta Weyoun, considered this an act of war, and launched an attack on Deep Space Nine itself. This battle is generally accepted as the true beginning of the Dominion War.
Cardassian and Dominion forces launched their attack on Deep Space Nine to wrest control of the station from the Federation. As UFP and Klingon forces were at the time launching their own raids on several key Dominion shipyards, this attack was successful, and the UFP was forced to abandon the station. However, under advisement 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. In 2374, while Dukat and Weyoun were trying to figure out a way to safely dismantle the minefield, Major Kira Nerys 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 Damar and Dominion forces.
In the late spring of 2374, Sisko was able to convince 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, so a large fleet of about 1200 starships was assembled to re-take the station. However, Dominion forces outnumbered the Federation fleet by nearly 3-to-1, and Dukat was very close to dismantling the minefield. With nothing left to lose, the Federation launched its assault, 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. In a desperate attempt to delay the thousands of ships ready to pour through the wormhole, Sisko asked the Prophets to intervene. They did so, causing the Dominion reinforcements to simply disappear. With Cardassian morale broken, they abandoned the station, and the UFP once again took control. The Federation victory by deus ex machina, and the murder by Damar of his daughter Ziyal 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.
Even with the Dominion leery of sending any more ships through the wormhole, the combined forces of the Klingon Empire and the UFP were barely holding their own. The Romulans, who had publicly declared their neutrality in the conflict were actually letting Dominion ships fly through their territory in order to make attacks upon the other two major Alpha Quadrant powers. After Dominion forces invaded and captured the planet Betazed, Sisko was convinced, and desperate, that the Klingon/UFP alliance would lose the Dominion War. He then connived, with the assistance of Garak, the only Cardassian with permanent residence on DS9 (and former master spy for the Obsidian Order), to plant false evidence of a Dominion plot to assassinate the Romulan proconsul. The Romulans bought the ploy, and allied themselves with the Federation and Klingons, thus improving the prospects of victory immensely.
Around the same time of the alliance with the Romulans, DS9's chief medical officer, Doctor Julian Bashir was made aware of the existence of Section 31, a covert intelligence 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.
With the Romulans assistance, the Alpha Quadrant Alliance was able to take from the Dominion the strategically important Chin'Toka system in early 2375, though science officer Jadzia Dax was murdered by Gul Dukat. The Dax symbiont however survived despite the death of its host body, and was rejoined with a new host to become Ezri Dax. Ezri remained aboard DS9 as the station's counselor.
Section 31, meanwhile, had also been busy behind the scenes. They managed to infect Odo with a virus that he then unknowingly communicated to the rest of the Founders by merging his form with that of the female shapeshifter's. The disease began to take its toll on the Founders in mid-2375, seriously damaging their ability to lead the war effort. Gul Damar, too, was growing increasingly frustrated with the seemingly stalemated war 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 prosecute the war successfully.
The Dominion's position became increasingly precarious, causing the female shapeshifter to form an alliance with the Breen, a relatively unknown space-faring species in the Alpha Quadrant. Their entry into the struggle temporarily turned the tide of the war back to the Dominion's favor. Breen vessels were equipped with a power draining weapon that rendered both UFP and Romulan vessels completely inert. Klingon vessels, initially vulnerable to this weapon, were able to be modified to resist it, however. With nearly two-thirds of the Alliance's fleet unable to fight against the Breen, the Dominion was able to stabilize its front lines, and re-take the Chin'Toka system, destroying Defiant in that battle. Breen and Jem'Hadar forces also managed to stage a lightning raid on Earth itself, destroying many Starfleet facilities and the Golden Gate Bridge in San Francisco.
The Klingons, now at the front lines of the battle almost completely alone, were instructed by Alliance commanders merely to hold the front while Alliance scientists tried to figure out a way to counter the Breen's energy draining weapon. General Martok complied with these orders, but the leader of the Klingon Empire, Chancellor Gowron began to fear that Martok's military prowess would eclipse his own. He stripped command of the war from Martok and assumed leadership himself, often placing Martok in no-win battles and throwing the Alliance's lines into chaos with increasingly dangerous missions in an attempt to cover himself in personal glory. The situation reached a head when DS9's strategic operations officer, Worf, challenged Gowron's leadership in open council. 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 decades of chaos, the war once again turned to near-stalemated conditions.
With the Dominion now giving more and more important military decisions, and even a few Cardassian colonies, to the Breen, Gul Damar, with the assistance of newly-promoted Colonel Kira Nerys and Garak, began his own underground resistance movement in an attempt to drive the Dominion out of Cardassian space. Damar was branded a rebel by the Dominion and went into hiding.
Around this time, Alliance scientists were finally able to find a way to defeat the Breen's special weapon, and it was decided that the Alliance was now in a position to take Cardassia itself, given that the Dominion was distracted by Damar's rebellion. The USS Sao Paulo was re-christened to become the second starship Defiant, with Sisko in command. A three-pronged strike led by Sisko, Chancellor Martok, and Admiral William Ross invaded Cardassian space in an all-or-nothing offensive.
Damar's attempts at fomenting a popular uprising against the Dominion was wildly successful, finally causing the Dominion to destroy an entire Cardassian metropolis, killing about 2 million Cardassians. This atrocity caused most Cardassian fleet captains to switch sides, aiding the Alliance's invasion of Cardassian space.
The Founders, facing extinction themselves, abandoned all pretense of being anything but polymorphic supremacists bent on imposing their version of order on the entire galaxy. Thus, they swore they would not surrender, promising a scorched earth war wherein any territory the Alliance managed to take would be so badly damaged, and so many people killed that Alliance victory would hardly be worth the effort. When the female shapeshifter discovered the treachery of the Cardassian fleet, she ordered the Jem'Hadar to exterminate the entire Cardassian race. Thus while Alliance--and Cardassian--starships fought for control of Cardassia Prime from space, the planet itself was being devastated by Jem'Hadar shock troops on the ground. A pyrrhic victory seemed inevitable for the Alliance, as nearly a billion Cardassian civilians were already dead.
However, Bashir and DS9's chief engineer Miles O'Brien managed to take the cure for the Section 31 created Founder's disease from the mind of one of its operatives. The cure was given to Odo, who then rushed to Cardassia Prime. In exchange for the Dominion's peaceful surrender, and the arrest of its Founder, Breen, and Vorta leaders for war crimes, the Alpha Quadrant Alliance allowed Odo to cure the Founders of their disease. A formal declaration of the cessation of hostilities was proclaimed in a ceremony aboard DS9, thus ending a conflict that had consumed nearly three-quarters of the galaxy for nearly seven years.
The fallout from that war goes mostly undocumented. The political ramifications are immense, as nearly every major Alpha Quadrant power, from the Federation to the Ferengi, underwent a dramatic shift in power. Cardassia lies in ruins, in far worse shape than what the Cardassians themselves did to the planet Bajor, and billions of people gave their lives in the struggle. Odo returned to the Founder's homeworld to teach them about the other races in the galaxy in an attempt to reform Founder society. The deceit which brought the Romulans into the war is still undiscovered. What will happen to the galaxy now? Only time (and the gods) will tell...
Thanks be to General Wesc, for his knowledge and assistance.
The people at Wikipedia have taken this writeup with my permission and really run with it. Check it: http://en.wikipedia.org/wiki/Dominion_war