The Thran Civil War, also known as the Thran-Phyrexian War, was the conflict in which the once mighty Thran Empire collapsed. It happened around ~5000 AR.
Prior to the War
Yawgmoth, a eugenicist, had been exiled from the empire because the eugenicists had stood on the side of the republicans, who had been defeated by the imperial elite. During his five years of exile, he committed many atrocities, such as setting loose plagues on entire countries to study its effect and vivisecting a mighty leader to learn about the inner workings of his body.
When the chief artificer Glacian fell ill and no Thran magic or medicine was adequate to help him, Yawgmoth was recalled from his exile. Yawgmoth quickly deduced that Glacian was suffering from phthisis and that it was caused by the powerstones on which Thran technology was based: soon more and more cases of the disease were found. Through his charisma and strategic genius, and the fact that only he knew how to create medicines to treat phthisis, Yawgmoth managed to become the most powerful person in the empire.
Declaration of War
The nations Yawgmoth had terrorized during his exile understandably did not like the fact that their one-time tormentor had seized control of the most powerful nation on the globe. Twenty-five minotaur, elven, dwarven, Viashino and catfolk nations allied themselves with humans of Gulatto Meisha and the Thran city-states of Losanon and Wington, who did not like the fact that Yawgmoth was taking away the power of the city-states. They gave the rest of the empire an ultimatum: Either Yawgmoth would leave, or the alliance would declare war.
The city-states decided to vote on the ultimatum, but the result was a tie: Nyoron, Seaton, Phoenon and Orleason voted that Yawgmoth could stay, whilst Chignon, Losanon, Wington and Halcyon voted that he should leave. This put the decision in the hands of the council of leaders: a group of healers, artificers, heroes, and other people who had done a great deed to advance the empire. Here the votes were equal, 13 against 13, up to the last two leaders. These were Rebbec (Glacian's wife) and Yawgmoth himself, both of whom voted that he could stay. Immediately afterward, Yawgmoth overthrew the council and had all elders and Alliance delegates imprisoned.
The first stages of the war went well for the Alliance, now known as the Thran Alliance. Orleason fell easily after the artificers of the city chose to side with the Alliance, and not much later Phoenon also fell after a short siege. Furious, Yawgmoth bombed the latter city, killing all the invaders and inhabitants inside.
But the next battle, on the Megheddon Defile, went differently. Yawgmoth's personal Halcyte Guard and people mutated in Phyrexia tore the other army apart, with only the artifact creatures standing a chance against them. At the same time, Yawgmoth fought and won a battle over the Null Sphere, which he used to turn all the artifact creatures against their masters, and finished the battle with a stonecharger that completely obliterated the Defile.
But minutes after the battle was over, two new Alliance armies appeared on the horizon. In the battle of Halcyon, Yawgmoth had planned to drop more stonechargers on them, and kill any that got into the city, but the artificers working on the Null Sphere sacrificed themselves to sabotage the device, thus when Yawgmoth dropped his stonechargers, he could not use the sphere to neutralize the death cloud they left behind and not only the opposing armies but all of Halcyon was destroyed as well.
What happened to the other city-states is unknown, however, Yawgmoth had given orders to his war caravels to drop other stonechargers on the cities that would not surrender. In any case, the Thran suffered so many losses that the empire fell shortly afterward.
Of the inhabitants of Halcyon, most had fled to Phyrexia. There they would be mutated, becoming the first true Phyrexians.
Rebbec had closed the portal to Phyrexia in the last moments before the cloud killed her, thus locking Yawgmoth and his followers outside Dominaria for millennia.
As for her husband, Glacian, his essence was locked away within a highly charged powerstone which would later become the Mightstone and Weakstone antiquity spoke of. This powerstone was what Rebbec used to ultimately seal the portal against the evil of Phyrexia.