The events known as the mission to the Prism unfolded in 19 BBY, subsequent to both the establishment of the New Order and the coup orchestrated by General Gentis. The goal of the coup was the assassination of Emperor Palpatine, Darth Vader, and many other high-ranking Imperial officers, in an effort to stop the never-ending deaths. Gentis successfully seized control of Coruscant by staging fake terrorist incidents, including one involving the poisonous gas Aorth-6. This gas eliminated numerous loyal Imperial personnel and soldiers; only Palpatine's command of the dark side of the Force allowed him to survive. Critically weakened, Palpatine was transported by Darth Vader, Moff Trachta, and Lieutenant Laurita Tohm to The Prism, a secret prison located in the Diab system, where they hoped to restore the Emperor's health. Once they arrived, Tohm conceived a strategy to reclaim the capital city by liberating the inmates of the Prism.
In 19 BBY, several weeks following the rise of the Galactic Empire, General Gentis was present at a military conference held on Imperial Center. While trying to escape the monotonous speeches of the various Moffs, he stumbled upon the Imperial Crematorium, where he witnessed the incineration of hundreds of dead Imperials every minute. He realized that even though the war was over, the Emperor's desire for war would never end, and he quickly began searching for a way to stop the pointless killing.
Some months later, cadets from six different academies across the galaxy traveled to the capital to participate in the inaugural graduation ceremony for Imperial officers. Gentis, a celebrated hero of the Clone Wars, presided over the event. Laurita Tohm, as valedictorian of the Raithal Academy, was awarded the rank of lieutenant by Gentis himself. Tohm was soon chosen to join Grand Moff Wilhuff Tarkin's fleet, but Gentis had different plans for the young officer. He instructed Ensigns Caul Gentis and Shens to ensure Tohm remained "out of harm's way". Tohm's comrades confined him within a prototype TIE/LN starfighter, which he initially believed to be a prank. However, it was the initial step in Gentis's coup, as he feared the promising officer would attract unwanted attention due to his prominence and physical deformities.
Later that evening, explosions resonated across kilometers of the city, destroying seventy-two Imperial targets in a matter of minutes. The officer's club, various Stormtrooper garrisons, the Comm Towers, and a supply depot were all reduced to rubble. Imperial Plaza became the epicenter of the ensuing conflict, as "terrorist" forces flooded the city streets, engaging the Empire's clone troopers. The stormtroopers were losing ground until Darth Vader arrived, bolstering their morale and forcing the enemy back. Amidst the chaos, Tohm escaped from the prototype starfighter by activating its ejector seat, landing in the middle of the battle.
During the fighting, Tohm encountered his wounded friend Shens. Shens pleaded with him to assassinate Vader, but Tohm rebuked him for excluding him from the plan and fatally shot Shens in the head. Tohm then paid his respects to Vader, who immediately recognized his courage and devotion. As they departed the plaza, another explosion ripped through nearby structures, releasing the deadly necrotic virus known as Aorth-6. Dozens of Imperials, including Royal Guardsmen, succumbed to the aerosolized virus, which caused their bodies to liquefy from the inside. Tohm, wearing a breathing apparatus he had retrieved from the TIE fighter, followed Vader inside. There, they discovered Palpatine and Moff Trachta mortally infected. Palpatine was using the dark side of the Force to resist the virus, but was struggling despite his considerable power. Vader accused Trachta of complicity in the conspiracy, but the Moff vehemently denied it, arguing that they needed to conceal the Emperor; the fear of his power was the only thing holding the Empire together. The three escorted Palpatine to a secret hangar beneath the Imperial Palace, where they placed him aboard a stealth transport.
Once they were safe, Trachta revealed that Gentis had feigned wanting to introduce his most promising students to the Emperor, but instead unleashed the virus. He then attempted to murder Tohm, claiming he distrusted him, but Vader disarmed him. The three debated where they could hide the Emperor, and Tohm suggested that Gentis's influence likely extended throughout all three Rims. Vader then recalled a location he had heard of, but he required more information, and he took Lieutenant Tohm to the Jedi Temple to obtain it. While they were gone, Gentis's engineers dispatched a command to every droid within five kilometers, ordering them to eliminate any Imperial officer they encountered. Aboard the Emperor's shuttle, a 2-1B surgical droid attacked Trachta, while Vader and Tohm were confronted by lightsaber-wielding Jedi training droids.
All three Imperials emerged victorious, and Vader led Tohm into the High Council Chamber and activated a holorecording of a Jedi Council meeting attended by Anakin Skywalker. Skywalker demanded information about the fate of the numerous prisoners he had captured during the war, but the Council dismissed his concerns as unfounded rumors. Skywalker persisted, vowing to obtain the truth from Supreme Chancellor Palpatine, but Obi-Wan Kenobi calmed him, although Skywalker departed in anger. The Jedi Masters continued the discussion after Skywalker's departure, revealing that the secret prison was a closely guarded secret, even from the Chancellor and the GAR. The Jedi believed that the Republic Security Force could not contain the Force-users, cyborgs, shape shifters and others they had apprehended, and that they would receive fair trials after the war. Kenobi expressed his displeasure but complied with the Council's decision, requesting permission to visit the prison himself. Master of the Order Mace Windu revealed the prison's location and cautioned Kenobi against bringing Anakin. Upon hearing this, Vader flew into a rage, destroying the Council chambers and declaring that the Emperor had been right, that the Jedi had been plotting against them from the start. He then urged Tohm to remember that the Jedi believed in too many ambiguities, while there was only the Empire, and everyone else.
Equipped with this new information, the Imperials set course for the Diab system, where the Prism was concealed. During the three-day journey, Tohm attempted to connect with the Force, but Trachta cautioned him against revealing any Force-sensitivity at that time. The two then shared the stories of their respective disfigurements; Trachta had been attacked by a Dark Jedi Padawan, while Tohm was the victim of a Separatist attack that claimed his family's lives and left him maimed. Trachta then remarked that traitors are only traitors if they do not succeed.

Despite encountering a perplexed Jedi Master and a contingent of security droids, Vader swiftly eliminated the Jedi, and the three quickly dispatched the droids. They transported Palpatine to the prison's medical facility, where they managed to halt the disintegration of his body. Tohm then accessed the prison's databank, discovering that it housed two hundred and eight prisoners, with over half having been apprehended by Anakin Skywalker. Vader informed Tohm that Skywalker had been an impressive Jedi, but that he had killed him, and instructed Tohm to erase the system's data. Trachta, however, sought a specific prisoner and enlisted Tohm's assistance in locating him. It was revealed that the Padawan who had so severely disfigured Trachta was imprisoned there, and the cyborg dedicated several hours to brutally torturing him to death.
Realizing that they could not trust anyone to contact for aid, Tohm formulated a plan and sought Lord Vader's approval: He proposed releasing all the prisoners of the Prism to form an army to challenge Gentis.
With a shortage of loyal or dependable soldiers, Tohm proposed to Vader that the prisoners within the Prism should be set free and used as a fighting force, which would enable them to take back Coruscant from General Gentis. Vader altered Tohm's concept, and instead of simply freeing the prisoners, he made 207 of them engage in combat against each other, along with Tohm and himself, for the privilege of serving the Galactic Empire. The resulting conflict was brutal and unrestrained, with heavy losses on all sides. Separatist sniper Shonn Volta allied herself with Tohm after rescuing him from General Ur'Loach, while Vader overcame Nax Cirvan, a fallen Jedi, who then yielded to the Dark Lord.
Ultimately, only thirty-three prisoners remained combat-ready, including Volta and Cirvan. Vader directed Trachta to explain to the survivors what service to the Empire entailed. Trachta informed the survivors that their past transgressions were now forgiven, but the motives behind them were not—they would now serve an institution that was not beholden to the "selfish" senators of the Republic, or the Jedi Order. The prisoners knelt before Trachta and the others, becoming Imperials through their submission.