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With the bulk of military power destroyed at DS9, Earth and other core worlds in the Dominion’s way lost and the remnants gone from the Federation the rest of the war would be a one-sided slaughter as Starfleet and the Klingons hopelessly continue to resist against impossible odds. For a while hit and run attacks manage to inflict some damage but not without great cost. In 2376 peace talks begin between the Federation Council and the female Founder. Though by this time the peace talks amount more to an unconditional surrender. The Federation agrees to cease all hostilities provided that the Dominion avoid atrocities against civilian populations. Still focused on the relatively stronger Klingon Empire, the Dominion happily agrees to this. For now. Before the peace talks were concluded, the opportunistic Romulans sign a quick alliance with the Dominion and attack the Federation, rapidly conquering various systems and declare war on the Klingon Empire.

Despite the realization that there is no chance to even form a moderately capable resistance against the Dominion, pride prevents the Klingons from agreeing to surrender as they engage in increasingly desperate strikes that start to look more like suicide attacks. By 2380 the Klingons have been hunted to near extinction and in their place the Orion Union and Kriosian Entente have risen as Dominion client states but with a form of independent on condition of continuing the hunt for surviving Klingons in the wastelands of what was once the most powerful empire. Things appear to settle as the Dominion imposes a new order on their new territories and research finally allows them to cure the virus created by Section 31. Some mercy being afforded to the Federation races when Odo in 2382 comes forward to take his role as Overseer. A role in which he amongst others prevents the subjugation of the Bajorans and holds back the more brutal instincts of the Vorta and Jem’Hadar as the final act of loyalty to the people who had taken him in.

In 2387 the balance of power shifts again when Hobus goes supernova and takes Romulus with it. Under the guise of helping their ally the Dominion commence incursions into their territory. By the time the Romulans know what is going on they are already surrounded with no alternative but to agree to become a client state as well. With the greatest threats to their power contained and the remaining independent powers to weak to form any threat in the eyes of the Dominion, the Alpha and Beta Quadrants have been truly purified.

The Founders have learned from historic records however that these races are far less docile than the ones in the Gamma Quadrant and especially human ingenuity has time and time again proven unstoppable. Behind the back of Odo they produce a virus much like the Teplan Blight, albeit a more advanced form. As Humans, Vulcans and Tellarite start disappearing, this new Blight appears among their worlds. Dominion propaganda is quick to express concern over this new illness and promises to commit scientific resources to finding a cure but proves unable to. Spreading the lie that the disease is contagious, other races are cautioned to stay away from Human, Vulcan and Tellarite worlds or risk exposure. On these worlds themselves the races develop extreme pain in the presence of any technology. Reverting them to pre-Industrial times as quarantines are imposed. A decade later a new species becomes visible on Jem’Hadar vessels and installations. Ranking even below the Jem’Hadar, these Nova serve as the Engineers of the Dominion. Incorporating the best of Humans, Vulcans and Tellarites they are deemed perfect for their new assignments but with any inclination to rebel suppressed.

By 2394 the first generation will have been raised without any experience other than being a subject of the Dominion, by 2500 most who remembered a time before the Dominion will have died. While resistance continues in the occupied territories and subjects continue to plot an eventual escape from Dominion rule, the Alpha and Beta Quadrant are mostly pacified.

The Remnants

Even with the secrecy involved, the mission of the fleet was still a dangerous one. To give them the greatest fighting chance Section 31 implements technology Starfleet would not have used before such as phase cloak while Starfleet Security works down a list of civilians deemed essential to continue the war effort. Taking these people with them whether they want to or not. Once the fleet is ready it starts on its journey not to return again anytime soon. By the time they have cleared Federation space, the true mission is revealed to the crews. There is some resistance at first at the thought of never again seeing their friends and families but discipline among both Starfleet and the Klingons makes sure those voices cease quickly. While the civilian population is more resistant, they too are made to comply as the Federation-Klingon command imposes increasingly strict measures to preserve order. All for the greater good. Before the fall of the Federation, contact had been made with the crew of the USS Voyager. Tapping into this same communication network the Fleet would continue to communicate with Voyager in its quest to find a place within the Delta Quadrant to rebuild and regain strength. Enemies are encountered on its way but the combined force is strong enough to overwhelm anything that tries to stop it. In 2389 the fleet meets with the Voyager in a star system home to several M-Class worlds without any civilizations on them. The system as well as its neighbouring systems are surrounded by a thick nebula that blocks sensors and most other means of detecting their presence. Voyager also did not come alone, having spent the last two decades leveraging contacts in the years made prior the ship aided in the rebellion of the Borg at Unimatrix Zero now assembled in the Liberated Borg Collective and an assortment of species joining the Delta Alliance for one reason or another but primarily to find a new home. Both of these bring with them valuable manpower, knowledge and experiences. The time to prepare a return commences.

The next few decades prove difficult, despite the unifying goals there are still major differences between the various factions. The union is close to disintegrating at various points and it is established that some action must be taken to keep it together properly. Captain Janeway, by that point one of the most experienced officers and one of the most respected people in the union pronounces Galactic Federation under military rule. Becoming the first Fleet Admiral, she combines the various militaries in the Galactic Fleet and uses Section 31 and Klingon Imperial Intelligence to act as a secret police of sorts to keep order.

With a return to the Alpha and Beta Quadrant continuing to be their sole focus the Galactic Federation expands the worlds it owns as its population booms, technology from all powers is combined to bring about ships stronger than the sum of its parts. Transwarp from the Borg, phase cloak from the Federation, disruptor technology combined with advanced phaser technology from the Klingons and Federation and so much more. Beyond this advancements continue as well as the best and brightest of the Galactic Federation develop such technologies as Transphasic Torpedoes and further advances in zero point based energy. Perhaps most dangerously the ban on Omega research is lifted as it is used to power both the Galactic Federation itself as well as weapons of mass destruction that may become needed to defeat the Dominion.

By 2600 the Galactic Federation would be barely recognizable as the species and civilizations it is composed of have integrated fully and even expanded within the Delta Quadrant. Increasing power has been consolidated in the Fleet Admiral as the Galactic Fleet finally becomes ready to return home.