The Jedi Civil War took place following a relatively long period of peace in 95 ABY, and saw the Jedi re-centralised around the Jedi Council. The conflict was also among the first stand-offs between the Empire and Galactic Alliance, and led directly to the Force Cold War.
Following the passing of the Daala crisis, the Jedi Order grew more diffuse, even as it unified the Jedi and other various factions and orders. Luke Skywalker's trip to discover the fate of Darth Caedus connected the dots, and, with the diffusion of the Jedi Order, saw satellite academies proliferate across known space. Systems with historic Jedi connections, such as Corellia, Kamparas, Bpfassh and Tannab, rebuilt their own schools even as Bothawui, Commenor and other systems saw home-grown movements sprout up. Largely self-policed, these elements interacted amongst themselves, putting down threats as they came across them, before handing over any darksiders they encountered to the Galactic Alliance, who dutifully secured them on Oovo IV.
This diffuse Order enabled the Jedi to deal with a great deal of threats as various teams were formed, defeating the Seyugi Dervishes, thwarting the resurrection of the Krath, driving back the Carbonite Sith Army and capturing Yu'Dor, the Yuuzhan Vong Sith. These victories, though massive, came with immense cost to the Galactic Alliance taxpayer, a cost the Senate was occasionally unwilling to pay. Various projects between rogue agencies of the GA and Empire came to light, projects which were just as problematic as dark side threats. When a Solo was placed in charge of one such agency, it was expected that the Galactic Alliance would grow more militant again, but the Jedi Master instead fled into exile after launching a Secret War against the Empire.
This diaspora sadly brought additional danger, as the lowers ranks of the Jedi became more disorganised and unruly. A few Jedi were imprisoned for misguided views of justice, and still more simply became media icons, even if they did not wish so. Few Jedi were regulated by anything other than their consciences. The Sith, wherever they lay, stayed hidden, content to sit and watch until they were strong enough to shatter the Jedi and Alliance.
But this Golden Age of the Jedi would come to a horrific end.
Midal saw a team of various Jedi from different schools - including an Imperial Knight - engage a team of rogue villains led by an Ember named 'Inferno'. While the team, live on the HoloNet, did indeed apprehend the majority of the group, Inferno unleashed her powers and consumed an entire bloc of Coruscant - and the buildings of the Upper City collapsed down. The Education District was devastated, and more than six hundred thousand civilians - more than a third children - died in the disaster. Jedi rushed from across the galaxy to help in the recovery, but the Senate quickly began assembling laws to resolve this once and fall. The Force User Registration Act - FURA - was drafted, demanding Jedi turn over themselves to the government, becoming true law enforcers and registering all their information for government use. The S.I.T.H. - the Strategic Intervention and Termination of Hazards group - prepared a battalion to arrest those Jedi who refused to sign-up. Hamner began to sidle up to the powerful Senate seat of Kuat, attempting to salvage the situation, gathering allies even as the diffuse Order began to fall apart. As SITH gathered more strength, the tensions began to rise.
When Durron fled from the S.I.T.H. Star Destroyer, the Anakin Solo, the factions began to assemble - the anti-registration group, the Guardians of Light, and the pro-registration group, the New Jedi Trials, formed, the latter led by Hamner. The Emperor declared him and his Imperial Knights faction neutral in the upcoming conflict, ditto the Empire itself. Skirmishes broke out as the Guardians set up rebel bases across the Alliance, several units of the Galactic Alliance Army aligning to assist them even as S.I.T.H. sought to shut them down. Particularly sharp battles were fought at Yavin, Hoth and Endor, traditional flare-ups which seemed to see the Alliance portrayed as a demonic force. The Trials began setting up new groups attached to the federalism of the Alliance, the Bothans, Corellians and other species amassing their own Force user orders under government auspices to augment the Trials offensive, the Trials defeating several threats at the same time - Inferno was ran down, a slaving ring on Pammant was broken, and a Ssi-Ruuvi terror plot foiled, usually as an aside to hunting for the Guardians.
But while the Guardians were difficult to defeat, they were heavily outnumbered, and even when Katarn aligned with the Guardians, were largely on the run. The Trials, on the other hand, had the capacity to create, and they did, activating secret projects to increase their numbers. Finally, after months of Guardian victories in the Outer Rim, with the Trials apparently instead focused on averting a war between the Empire and Alliance, the Trials turned their full attention to the Guardians. The Guardians had used the time to net a growing following, with more and more of the Army siding with them as S.I.T.H. became more like the GAG and GAS every passing day in order to counter the loss of the Trials. The only battle against this trend was the surprising loss of a Guardians base on Folor, surprising because the Guardians had no indications that the Alliance had noticed it, and they had no information as to how the base fell. Despite this, the Guardians steadily collected resources to strike at the Jedi Temple on Coruscant - though information began to seep through that the Trials had constructed a secret prison in Otherspace based upon an elderly Golan IV battlestation, and thus far from the reach of the Guardians - it was accessible only through portals on Coruscant and Ossus, both of which were defended by vast GA and S.I.T.H. resources.
The Battle of Kiris
The off and on skirmishing came to a halt when the Kiris Asteroid Belt - home to famed Corellia yards which constructed a secret assault fleet during the Second Galactic Civil War - were attacked by a rouge force of YVH hunter droids, taking the workers hostage and forcing them to complete the Corellian Dreadnaught at the yard for their use. The Guardians of Light rushed to assist, the Trials caught off-guard hunting for the Guardians in the Tion Cluster. It was a trap. The Trials had control of the droids all along, and S.I.T.H. blockaded the asteroids even as the New Jedi Trials advanced, unveiling weapons they had tested at Folor - Dark Jedi and Dark Side Adepts controlled via Yuuzhan Vong slave seeds, furnished to the Trials by Yu'Dor, now working for the government. Battle broke out despite the clear lack of parity between the Guardians and Trials - and the Trials still struggled to contain the Guardians at the arena of their choosing. As Hamner struggled against Durron and Katarn, the final secret weapon of the Trials was unleashed - a clone of Luke Skywalker himself.
It was this moment that defined the Civil War, and widened it dramatically. Luke killed Katarn in a no-holds barred duel, even as several key enslaved villains began to turn against their new masters. Unnoticed at the edges of the battle, the seeded villains began to gather the munitions to totally destroy the asteroids. While eventually thwarted by Solo, who had decided to join the battle to keep an eye on things, Solo himself had been discredited, and nothing he could do could amend that. With the death of Katarn, the Trials fissioned mid-battle, several Jedi giving up their lives to hold back the Luke clone. The Guardians managed to escape in the confusion, and the Trials and the SITH bound Luke, before too fixing him with a slave seed.
The True Enemy
Yu'Dor had anticipated this, and in the confusion of the Battle of Kiris, managed to escape her cell. The slave seeds were naturally telepathic, and with no central yammosk to control them, created their own hive mind - which would seek its own objectives. The seeds could also act as a meld of sorts, funnelling Force sensitivity to wherever was needed. While Solo made attempts to convince the Trials and Guardians to the new threat, nothing came of it, and the Guardians, bulked up by a wave of defections in the wake of Katarn's death, continued with their planned attack on Ossus, seeking to end the war by freeing all the interned Jedi. Solo recruited several Jedi to his cause, and advanced on behind the Guardians attack, the seed mind actively trying to trap everyone in Otherspace - even while assisting the Trials to sell the hoax. When it became apparent that the seed mind would fail, it turned it against all the Jedi, capturing whole swathes of them. While the surviving Trials and Guardians managed to escape, Solo sacrificed himself to seal the doorway to Otherspace, and to the prison - trapping more than two thirds of the Jedi Order in Otherspace.
The blow was a disaster to the Jedi community, who promptly spent the next month re-establishing itself on Corellia, while the Senate announced that FURA was placed on hold for the time being - at least until the dust had settled and the largest faction was decided. Finger pointing was beginning to flare up, but without SITH to back him up, Hamner had little else he could achieve other than work with the Guardians for now, themselves distrustful of the Trials. The federalist groups at Fondor, Corellia and Bothawui were slowly recovered, but it seemed a matter of time before the war restarted.
Exactly one month after the Battle of Ossus, portals to Otherspace began opening across the galaxy - and flights of small craft emerged from them. The yards at Kuat were targeted, and several warships and fighters stolen - before vanishing back into Otherspace with a quarter of the yards stolen. Other raids, at Roxuli and its ore mines, Kril'dor and its Tibanna mines, and Roche and its munition plants, rapidly began to see an invasion force amassed in Otherspace, with the Trials and Guardians fighting a seed mind which absorbed all the thoughts of the prisoners it took, and all the Jedi it kidnapped. When it became evident that the Hive had gathered the resources required to invade, the Jedi advanced on Coruscant - anticipating the offensive to follow. It did, through the portal at Coruscant and in orbit, a motley armada emerging in massive numbers - the hive mind had enabled the Jedi and slaves to reach Killik-level construction. Similarly, thousands of warships struck across the Alliance, hitting systems such as Eriadu, Balmorra, Kuat, Hapes and Mon Calamari - devastating the Alliance and seeing whole swathes of territory fall to the Hive. The Hive could move the Force accordingly, and even though the Jedi managed to successfully defend Coruscant and defeat the Luke clone - barely - all appeared lost. However, from amongst the Jedi and Dark Jedi they recovered in the battle, the Jedi gained enough allies to launch a final offensive, placing Luke in carbonite for now.
It became evident, however, that the Hive was re-establishing itself around a central mind, which could no longer be diffused through the slave seeds because it was now too immense. The captured seeds enabled the Jedi to work out the location of the mindworld this new Hive Empire - Denon, in the Inner Rim. The Jedi gathered their strength around them, even as the Hive did the same thing - gobbling up much of the galaxy. While Bothawui, Fondor, Corellia and Hapes managed to hold off the invaders, the Empire began to struggle against the massive forces of the Hive. In a very short time, the innumerable sector fleets of the galaxy were vanishing, leaving several fortress worlds that were becoming more isolated by the week. A year since the Midal Disaster, and the Alliance appeared poised near the edge of collapse, the Twelve Fleets hunkered down around Coruscant even as the personal navies of the member worlds were hunkered down. The government collapsed, and the Jedi were forced to advance on their own - a full offensive on Denon.
The Battle of Denon
The Battle of Denon was a clash of violence. Jedi fighting infected minds, overwhelming the slave seeds and disabling their users as humanely as possible. As the Hive fought more desperately, the Jedi struck upon using Vongsense, a skill that the Jedi and Dark Jedi who had been saved mastered, to break apart areas of the slave mind, disabling waves of infected enemies. Yu'Dor was freed from the slave mind and fled, even as Hamner and Durron, side-by-side, faced off with the 'face' of the Hive Mind - Solo. Touching the immense power of the Hive, Solo engaged the surviving Jedi and Dark Jedi - a brutal duel to the finish which eventually saw the Hive crack - and driven back. Without its central mind, the web began to collapse, and the slow rehabilitation of the Jedi and Dark Jedi began. The situation took four months to rectify, and even then much of the galaxy was ruined, and the Galactic Alliance was irrevocably shattered. SITH had taken this opportunity to recover, and the new government, reforming volunteer Dark Jedi into the Dominion, began to press for registration, arguing even more stridently that had the Jedi Civil War never occurred, this crisis would never have grown so immense - in a face-saving action designed to reunite the Alliance. While worlds did generally rejoin the Alliance - though the Empire again expanded its territory even more - the cooperation was largely lost, and the Alliance faced a crisis. The Trials were began anew, Force users which had defended their homeworlds making the heart of Force Sensitive units - the Bothan Hunters, the Corellian Skirmishers and the Hapan Knights being the largest of the said organisations. Re-integrated into the Trials, Hamner called for the surrender of the Guardians, many of which were still nominally in prison in Otherspace.
Efforts to broker a continued truce failed when SITH attacked the Guardian base on Kashyyyk, and the Trials were forced to retake their authority within the organisation to control it. The Dominion became a key unit, defending Fondor successfully from the Guardian offensives. The Guardians were weakened, and rightfully so, before recruiting Shi'do Force users to pierce the net around the newly reestablished Ossus portal. The Guardians beseeched the Emperor for assistance, who had himself decided it was time for the Empire to resolve the crisis once and for all, unhappy with the GA handling of FURA in general. The Dominion, Trials and SITH prepared a trap at Ossus - which the Guardians seemingly felll straight into. As it was, the Guardians freed all their captive allies, and this rapidly turned the tables against the Trials and their own allies. The Guardians managed to portal out of Otherspace to Coruscant, where the final battle took place. The Guardians began to struggle in the expanded environ, before the Imperial Knights intervened - declaring war against the Trials and Dominion, and specifically not the SITH and Alliance itself. In the subsequent fighting, Hamner engaged Durron again, and Emperor Fel engaged Luke. The Emperor triumphed over Luke first, and he was dragged away. The Trials began to collapse under the strain, the SITH unable to fight back at the Imperial Knights for fear of angering the Empire's navies, which had arrived to safeguard their Emperor - and were of similar military strength to the GA. Central authority on Coruscant collapsed again, and it appeared that Durron, poised to kill Hamner, had succeeded in overthrowing FURA.
However, Durron acknowledged that he had lost the arguement - he wasn't winning the debate, just the war. The Alliance was scupered, the Dominion routed and retreating to defend Fondor, and the Senate District aflame. Despite being remarkably close to victory, Durron surrendered to the SITH, and ordered his Jedi to stand down. The Emperor and his Imperial Knights departed, and the Guardians started the humiliating and difficult road towards re-integration. The subsequent death of Durron, just before his court hearing, radicalised several surviving Guardians - pushing many of them deeper into hiding. The Trials had won, and were proclaimed the Jedi Council - the Trials themselves creating new Force orders or resurrecting old ones locally - and re-establishing central authority with SITH assistance.
The Jedi Civil War raged for nearly two years and devastated the galaxy. Its consequences were, largely, minor, though they continued to create echoes which reverberated until the close of 100 ABY. The largest of its issues were the movement in military and Force power. Bothawui, Corellia and Hapes grew interested in their own Force cults, and Denon sought to militarise itself so that it would never be attacked again - resurrecting ancient war fleets which had been inactive since even the Yuuzhan Vong War. Many systems remilitarised in response to the damage they had took, even as Alliance central authority was re-established with the Council equally. The escape of Yu'Dor would prove a catastrophe in the long term, but in the short term the use of Shi'do Force Users to provide the Guardians with victory would reveal an alliance between them and geneticists on Arkania and Lurr, resulting in the short-lived but devastating Secret Invasion later in 97 ABY, and the establishment of the Dominion group would enable the Sith to regain a footing of power - leading to the year long Dark Reign and the Force Cold War.