Zaras launched a series of campaigns to restore order. As what was left of Tephrike's parliament and cabinet refused to acknowledge her claim, fierce fighting ensued in the capital of Palmyra, and the Presidential Palace was shelled. The death toll was high. However, many fatailities were not due to combat, but due to disease and malnutrition. Tephrike had always been dependent on trade, but this was obviously no longer an option in the Dark Age. Many foodstuffs and other essentials had been imported. With large swathes of the populace at the risk of starvation, the Jedi Lord implemented a policy of requisitions. All spheres of economic life would be nationalised, those who did not work would be conscripted into labour battalions and hoarding would be punished severely.
It came to clashes with the Gungans, who were accused placing their own selfish desires above the greater good and had granted asylum to renegades who'd stood with Parliament. The punitive campaigns and requisitions took their toll on the Jedi. Unable to cope with the strain - or rationalise the disconnect between the Jedi beliefs and their bleak reality - some went insane, deserted or fell to the Dark Side. Feeling that she could not relinquish authority despite having 'restored order' to most of the planet, Zaras broke her promise to step down. A rump Parliament had been convened to implement a new order and attempt to negotiate a settlement. But when several of the delegates criticised the Jedi Lord's actions, her soldiers forcibly removed them from the building. Elections were indefinitely suspended. Zaras Dant was assassinated by one of her own bodyguards. Her death led to a power struggle between the factions, out of all of which Jedi Tyian Kree emerged victor.
A Devaronian Jedi Sentinel, Kree was very ambitious - and had unknowingly fallen to the Dark Side. Obsessed with the idea that the Plague had been a Sith conspiracy and that agents of darkness lurked everywhere, she saw the uprisings sparking across the planet as confirmation. The infrastructure for a dictatorship had already been put into place by Zaras, but Tyian finished what her predecessor had started by implementing a totalitarian theocracy. For it was the only way to ensure that the Light would not be eclipsed by the forces of Darkness. In order to save the last vestiges of civilisation, the Jedi would have to harden their hearts. Furthermore, they would have to spread their beliefs to the common people, lest they become pawns of the Darkness.
A harsh crackdown followed, as her rule was challenged by Jedi who believed she was going too far, genuine darksiders and secular or secessionist rebels. On both sides, the war became increasingly savage. Abandoning the devastated Palmyra, she ordered the construction of a new capital, which would in time be known as Nexus City. By the time of her death, she'd secured most of the planet, though insurgents continued to challenge the Jedi's rule from hideouts in the jungle or underwater. To bring the rebels to heel, Kree laid siege to a Gungan city that housed rebels, but ended up dying from a heart attack.
The Jedi commanders met in secret conclave and elected a new Jedi Lord, who also assumed the title of Grand Master. After all, as far as they knew, they were the last Jedi. The new realm would be called the Dominion of Light. Palmyra was abandoned for good and Nexus City became the new capital. Here, the population could be monitored and indoctrinated. Here, the Grand Master reigned from a Jedi Temple modelled after the one on Coruscant...though said Grand Master increasingly became a puppet of the Battlemasters. Moreover, the Jedi began to make use of the medical cloning facilities that had been built before the collapse. Of course, since these had originally been designed with animals in mind, many clones ended up being of inferior quality. Many had a very short life expectancy or were afflicted with clone madness. Over time science and magic became one and the same, and the ancient systems were surrounded with rituals and lore.
A group of rebellious clone troopers deserted the regime and joined with Gungan and Nautolan insurgents to found the Republican Guard, as the indoctrination backfired. While Jedi idealised a warped Jedi order, believing that they were the inheritors of Mace Windu and Lord Hoth, these clones idolised the Republic. Red Coral City became their new headquarters. From there they would launch raids and skirmishes in their bed to liberate the planet from its theocratic rulers. Rebellious Jedi students, drunk on the power they wielded in the remote provinces, declared war on the Light and founded the Disciples of the Vader. The leader of this cult had been grown in a lab and was more than a little mad, believing that the Vader spoke to him in his dreams and had given him a mission to destroy the Light. Using primitive sorcery, they amassed an army of beasts and undead, using them to overrun a number of settlements, before failing at the ruins of Palmyra, after being lured there by the Jedi Battlemaster. However, disease and lack of supplies took their toll on the Jedi army as it pursued them. The Vader cultists would eventually claim an old castle as their stronghold, using slave labourers to restore it and augment its defences. Reflecting the racial tensions that had plagued Tephrike for so long, they also adopted a human supremacist ideology.
Lacking the means to directly overthrow the theocratic regime, they became raiders, slaveholders and marauders. Increasingly, the Windian Jedi Order grew bloated and corrupt. In the territory it managed to seize, the Republican Guard restored semblances of the rule of law and even democracy on the local levels, but also persecuted Force-users. Given the harm Forceful beings had done, one could not blame them. Both rebel factions remained implacably hostile to the Dominion of Light, but refused to cooperate due to their mutual animosity. This probably helped keep the regime afloat, even though its power was diminished under the reign of a succession of weak Grandmasters. For those who lived within the heartland of the Jedi's dominion, there was a degree of stability and security, albeit at the price of living under a totalitarian regime. Over time, what knowledge the Tephriki had once possessed of the outside world faded into the realm of myth.
Time passed, and most of the rest of the Galaxy emerged from the Dark Age. Great powers tried to exact their dominance upon the known worlds, empires rose and fell, but Tephrike remained in a state of stasis. The Netherworld Incident caused an outburst of religious fervour, as suddenly tons of people vanished. In the territory controlled by the Windian Jedi, the event was blamed on nefarious darkside magic. Clearly collaborators and Sith sorcerers had caused the disappearances, even though the Vader fanatics had been affected, too, and even underwent a civil war. The ensuing purges weakened the Windians, allowing their rivals to make some territorial gains. It remains to be seen which side will prevail and be able to enforce its vision upon Tephrike, and whether the planet's population will finally get lasting peace and the chance to recover.