Sith–Imperial War

The origins of the war can be traced back to the Ossus Project, during which the New Jedi Order successfully advocated for the Galactic Alliance's consent to allow Yuuzhan Vong Shapers, under the direction of Master Shaper Nei Rin, to utilize a deserted area of Ossus, one of the Order's oldest strongholds, as an experimental site.

The intention of the project's advocates, including Jedi Master Kol Skywalker, a prominent figure within the Jedi Council, was to assess whether Yuuzhan Vong terraforming techniques, akin to those that had transformed Coruscant into the Yuuzhan Vong's temporary homeworld known as Yuuzhan'tar (27–29 ABY) decades prior, could revitalize the barren and ravaged planet. Skywalker anticipated that success would enable the application of this process to rehabilitate ailing worlds, thereby reshaping the galaxy's perception of the Yuuzhan Vong. The experiment yielded positive results, restoring Ossus to a state of flourishing life. Upon the Jedi's revelation of these outcomes to the wider galaxy, numerous worlds competed for the opportunity to restore planets devastated by the preceding Yuuzhan Vong War which occurred a century prior.

Ultimately, one hundred planets were selected for terraforming. Yuuzhan Vong Shapers, accompanied by Jedi, commenced their work, initially achieving remarkable outcomes. However, the One Sith intervened unexpectedly. Upon the orders of the cult's leader, Darth Krayt, and with the assistance of a rogue Yuuzhan Vong agent, Zenoc Quah, the One Sith covertly sabotaged the terraforming process on these planets, including Wayland. This resulted in deformed plant growth and the emergence of painful bony growths on the inhabitants' skin, reminiscent of the Yuuzhan Vong's enslavement of populations.

The Yuuzhan Vong were taken aback, as none of the preliminary experiments on Ossus had indicated such mutations. Master Shaper Rin dedicated herself to uncovering the cause and rationale behind these developments. The Jedi immediately suspected sabotage but lacked knowledge of the perpetrator. Across the galaxy, however, blame was directed towards the Yuuzhan Vong. Lingering animosity towards the instigators of one of the galaxy's most devastating wars fueled suspicions that the Yuuzhan Vong had resumed their crusade through alternative means, precisely as the Sith had intended. Despite this, the Jedi remained convinced of the Yuuzhan Vong's innocence and persuaded the Alliance to defend them against domestic criticism. This decision incited anger among Alliance member worlds, leading many to secede or declare neutrality.

The Fel Empire considered this to be unacceptable, and seized an opportunity presented by the erosion of confidence in the Galactic Alliance. Following the signing of the Pellaeon–Gavrisom Treaty in 19 ABY, the Imperial Remnant had concluded its conflict against the former Rebellion, and the Yuuzhan Vong invasion had fostered collaboration, or at least amicable rivalry. However, the Moff Council, the Empire's governing body, still harbored hard-line adherents to the old order who sought to restore the Empire's dominance, irrespective of the peace treaty. These individuals now advocated for retribution and, invoking the Treaty of Anaxes, declared war on the Galactic Alliance. The peace that had been achieved at great cost was undone by the actions of the new Sith Order.

Anticipating potential consequences, the Jedi High Council mandated the establishment of the Hidden Temple at the onset of hostilities, with its location selected by Nat Skywalker to provide the Jedi with a sanctuary.

From the outset, the Alliance faced significant disadvantages. Its defense of the Yuuzhan Vong had alienated numerous member worlds, whose populations still harbored resentment from the Vong invasion, leading many to withhold support from the GA. Consequently, the Alliance confronted both a secession movement and a widespread war. The Empire capitalized on this situation, enticing disaffected worlds into the Imperial fold and weakening the GA government. Other worlds opted for neutrality. Thus, the war commenced with the Empire holding all the advantages. However, Emperor Roan Fel himself displayed a lack of enthusiasm, reluctantly declaring war and withholding his full support. He even prevented his Imperial Knights from engaging. This decision resulted in the Empire's initial struggles during the early stages of the war. An example of this was the Battle of Corulag where Oron Jaeger, an Imperial Army General of the 501st Legion sustained a head injury during the battle, necessitating cyborg augmentation.

Concurrently, the Mandalorians, now under the leadership of Mand'alor Chernan Ordo, were tasked by the Galactic Alliance with defending the planet Botajef and its shipyards against the Imperial Army until the Galactic Alliance Fleet arrived with reinforcements. However, during the Battle of Botajef, a traitor named Yaga Auchs emerged within their ranks. Auchs, serving an unknown master, sabotaged communication with the Alliance fleet and betrayed his comrades, leading to the Mand'alor's death. Usurping the title for himself, Auchs exploited his authority as the new Mand'alor to order a retreat, surrendering Botajef to the Empire and withdrawing his people from the war. As Auchs retreated, Hondo Karr and Vevec, the father of Karr's wife, were stranded on Botajef. With Imperial soldiers closing in, Karr donned the armor of a deceased stormtrooper, while Vevec sacrificed himself to aid Karr's disguise as the last survivor of his unit.

By 128 ABY, one year into the conflict, the Fel Empire was struggling. Despite the Alliance's disadvantages, the Jedi were compensating effectively. Furthermore, Roan Fel's refusal to allow the Imperial Knights to participate weakened the Empire's ability to counter the Jedi. However, the Sith soon integrated themselves into the war. Through the ambitious Director of Imperial Intelligence, Grand Moff Nyna Calixte, the Sith approached the Empire and forged an alliance. When the Sith openly declared themselves, the Jedi realized their involvement in the sabotage of the Vong terraforming projects. Although the Jedi lacked definitive proof, subsequent events confirmed their suspicions, even among members of the Imperial camp, including Emperor Fel himself. Fel harbored a personal hatred for the Sith but was overruled by the Moff Council, as no Emperor had wielded absolute authority since Palpatine's era. The Council, eager to exploit any advantage to restore Imperial dominance, readily accepted the alliance. Upon discovering the truth, the Yuuzhan Vong initially felt relieved that their gods were not responsible, then resolved to reverse the damage caused by the sabotage. Shaper Nei Rin traveled from Ossus to uncover the Sith's methods, hoping to discredit them and end the war.

After three years of intense warfare, the Galactic Alliance was depleted, while the Sith grew in power and strength, independently producing and deploying their own starfighters. Under the command of Grand Admiral Morlish Veed, Calixte's lover and a participant in the Sith conspiracy, the Imperial fleet inflicted a decisive defeat on the Alliance at the Battle of Caamas. Admiral Gar Stazi, an Alliance task force commander at Caamas, was compelled to execute a strategic withdrawal to preserve his ships.

Veed's declaration of victory effectively signaled the war's end. With the Galactic Alliance Defense Force decimated, Coruscant, the capital, was left undefended. The Alliance had no option but to surrender, and its territory was incorporated into the Empire. However, the Galactic Alliance Core Fleet, under Admiral Stazi's command, remained active and continued to resist the Empire.

Despite knowing the Jedi would refuse, Emperor Fel demanded their surrender and submission to the Empire. Some complied, joining the Imperial Knights. However, the majority, remaining loyal to the Force, refused to align with the Sith and retreated from Coruscant to their temple on Ossus. The Sith pursued them, and Darth Nihl led a brutal assault, aided by Imperial forces under Moff Rulf Yage. The Massacre at Ossus scattered the Jedi across the galaxy, though the Order was not entirely destroyed. As the Sith attacked before the entire Order could assemble on Ossus, approximately half survived and went into hiding. Nei Rin returned to Ossus the following day with evidence of the Sith's involvement in the projects' sabotage, but it was too late to prevent either the war or the massacre.

Shortly thereafter, the Sith, seeking direct control of the galaxy, launched a coup against Emperor Roan Fel and his Imperial Knights. After eliminating what he later discovered to be a double of the Emperor, the Attack on Emperor Fel succeeded, with Darth Krayt seizing the Imperial throne and restoring Sith rule over most of the galaxy for the first time in over a century. A new Sith Empire emerged.

However, some worlds and systems remained loyal to the deposed Emperor Fel, who managed to reclaim the heavily fortified world of Bastion. He established it as his acting capital, creating a rival faction to the Sith Empire, plunging the Galaxy into civil war once more. Fel later formed an alliance against the Sith with the Galactic Alliance Remnant. The Jedi subsequently joined this coalition. An unexpected event occurred when Krayt was seemingly killed by his advisor after a duel with a female Jedi and an ancient Sith Lord.