Shortly after the conclusion of the Grand Festival of Empress Vaylin, the Alliance Commander, accompanied by Theron Shan and Lana Beniko, embarked on a mission. The purpose of this undertaking was to prevent the Eternal Empire's control from shattering her mental conditioning on the desolate world of Nathema. Theron piloted their craft to the Nathema system, setting Lana and the Commander down near the Sanitarium, seemingly the only structure showing any indication of life on the planet, which had been devastated by the Ritual of Nathema. After dealing with the Horizon Guards guarding the entrance, the Commander and Lana entered the Sanitarium. Inside, they uncovered details about Vaylin's conditioning through holorecordings left behind by Anomid scientist Jarak. Regrettably, they were too late to intervene, as Vaylin had already been subjected to the ritual by Jarak, which spiraled out of control, resulting in her power incinerating those nearby. Jarak fled for his life, encountering Lana and the Commander and offering to guide them to a safe haven from the energy surges. Together, they reached the Immortal Emperor's Vault, where Valkorion had stored artifacts deemed too dangerous even for himself, managing to enter just in the nick of time. With the power systems fried, Beniko and the Commander proceeded to activate the emergency power generator, while Jarak met his end at the hands of a vault guardian. Deep within the vault, the Commander and Lana stumbled upon a significant discovery: Dramath's holocron, containing the essence of Valkorion's father, Dramath. Dramath revealed that the holocron possessed the potential to eradicate Vitiate permanently. Securing the holocron and unlocking the vault door, the two learned from Theron that Vaylin had already departed the planet and that the Sanitarium was on the verge of collapse. The Commander and Lana hurried outside, where Theron retrieved them. However, their respite was short-lived, as Bey'wan Aygo informed them that Vaylin had launched an assault on Odessen.
Vaylin, the Eternal Empress, became cognizant of the mental conditioning that Valkorion had imposed upon her. Consequently, she directed Jarak, the Anomid scientist who had administered the conditioning, to discover a method to undo his work in the Sanitarium on Nathema. During the Grand Festival of Empress Vaylin, Jarak informed the Empress of his breakthrough. Vaylin, who had suffered humiliation at the hands of the Alliance Commander when her conditioning was used against her, departed Zakuul aboard her personal flagship and journeyed to Nathema. Concurrently, the Alliance Commander, who harbored Valkorion's spirit within, experienced a fragment of Valkorion's memory depicting Vaylin's initial return to Zakuul after years spent on Nathema. Upon hearing this from the Commander, former Emperor Arcann, Vaylin's brother and recent addition to the Alliance, identified Nathema as the location of Vaylin's conditioning. He surmised that her return was prompted by a means to break free. Nathema, a Void in the Force since Vitiate eradicated all life with his ritual, was deemed too perilous for the newly redeemed Arcann. Thus, the Alliance Commander, accompanied only by Lana Beniko and Theron Shan, two of their closest advisors, set out for Nathema.
Theron piloted their shuttle to the Nathema system, where Lana began to sense the effects of the Force void even before landing. Even Valkorion's power was diminished in this place, although he assured the Alliance Commander and their companion that he would shield them from its worst effects. The shuttle's sensors identified the Sanitarium as the only structure displaying signs of activity. Theron dropped off Lana and the Commander near the Sanitarium and then moved the shuttle to a safe distance. Meanwhile, Vaylin landed at the entrance to the Sanitarium with a contingent of Horizon Guards, where she was greeted by an Abyssin Keeper, who informed Vaylin that Jarak awaited her inside his laboratory.
The Empress ordered the Horizon Guards to remain outside and ventured into the habitat where Jarak conducted his twisted experiments. Jarak arrived to witness Vaylin slaughtering three of his mutated Acklays and informed her that everything was prepared for her in the main lab. Simultaneously, Lana and the Commander approached the entrance of the Sanitarium, where they eliminated the Horizon Guards and followed Vaylin inside. Within the Sanitarium's walls, Lana and the Commander proceeded to defeat skytroopers, Nathema Zealots, and Keepers who stood in their path, while also learning about Jarak's role in Vaylin's conditioning from his holorecordings.
In the main laboratory, Jarak had prepared a large circular arena encircled by massive energy orb nodes. He explained to Vaylin that the process to break her conditioning would be even more extreme than before, with no one else having survived it thus far. However, Jarak also assured the Empress that her unparalleled strength in the Force would provide her with a chance that no one else had. Vaylin agreed to proceed. The pillar orbs pierced Vaylin's body with energy beams, inflicting immense pain and causing her power to surge uncontrollably. As Vaylin struggled, the Force blasts emanating from her body vaporized several Keepers and Zealots, while Jarak fled the room to save himself.
He encountered Lana and the Commander and quickly explained that he alone knew the location of a safe place, requesting that they escort him there through the beasts driven mad by Vaylin's power. To ensure their mutual survival, Jarak led them to the Emperor's Vault in the Sanitarium's lower levels, where they barely managed to enter to escape the energy blasts that ravaged everything outside and fried the vault's power circuits. Throughout this ordeal, Vaylin was alone, at the mercy of Jarak's inventions, and continued to endure unbearable pain. Finally, determined not to perish in the place she loathed so much, Vaylin mustered all of her remaining strength and overpowered Jarak's machines, causing them to explode one by one and freeing her from their grasp. As soon as the pain ceased, Vaylin could sense that her bonds had been broken and departed the surface of Nathema.
Inside the vault, the spirit of Valkorion informed the Commander that Vaylin had broken free from her bonds before fading due to the Force void that permeated the area. Jarak informed the Commander and Lana about the vault's backup power generator, warning them to beware of the vault's ancient guardians. After restoring the power, the Commander and Lana made a significant discovery by finding Dramath's holocron, which still contained the essence of Valkorion's father, who had been killed over 1300 years ago. Dramath recounted the history of his torment and revealed that the holocron possessed the power to destroy Vitiate once and for all. The Commander instructed Lana to safeguard the holocron, as Valkorion would become aware of the Commander's actions as soon as they exited the vault. Jarak was killed by a Vault Guardian, and the Commander and Lana had to fend off three large Voreclaws before finally opening the vault door. Theron informed them that Vaylin had already left the surface, and the two rushed to escape the Sanitarium, which was now on the verge of collapse. The Commander and Lana made their way to the landing platform outside, where Theron picked them up, leaving Nathema behind.
The Alliance's initial objective ended in failure, as Vaylin succeeded in breaking her chains without even realizing that the Alliance had attempted to stop her. Upon returning to her flagship, Vaylin demonstrated her full power by Force Crushing everyone on the bridge and using it to remotely trigger the Sanitarium's destruction, before ordering her ships to depart Nathema's orbit. She then immediately ordered the Eternal Fleet to launch an assault on Odessen, intending to eliminate the Alliance for good. However, the Alliance managed to locate and obtain Dramath's holocron, a relic that would prove crucial to Vitiate's ultimate destruction. After learning from Bey'wan Aygo about the attack on Odessen, Theron immediately returned the shuttle to their base. Having sensed her daughter breaking free from her mental bonds, Senya Tirall awoke from her long coma on Odessen and joined the ranks of its defenders alongside Arcann.
During Chapter VII: Into The Void the player must decide between freeing Lord Dramath from his holocron prison and allowing him to pass on for Light Side points, or keeping him bound for Dark Side points. The latter option enables Dramath to join as a temporary companion during Chapter IX: The Eternal Throne, significantly easing the fight against Vaylin's spirit.