Having become aware of the mental conditioning imposed on her by Valkorion, Eternal Empress Vaylin ordered Jarak, the Anomid scientist responsible for it, to find a way to undo the work done by him in the Sanitarium on Nathema. During the Grand Festival of Empress Vaylin, Jarak informed the Empress that he made a breakthrough and Vaylin, who suffered a humiliation when the Alliance Commander used her conditioning against her, departed Zakuul and traveled to Nathema on her personal flagship. Meanwhile, the Alliance Commander, who hosted Valkorion's spirit inside their head, experienced a portion of Valkorion's memory in which Vaylin first came back to Zakuul after spending years on Nathema. When the Commander mentioned it to former Emperor Arcann, Vaylin's brother who recently joined the Alliance, he identified Nathema as the site of Vaylin's conditioning and deduced that she was only coming back there because she found a way to break it. Nathema was a Void in the Force ever since Vitiate killed all life on it with his ritual, too dangerous for recently redeemed Arcann to visit, so the Alliance Commander departed there with only Lana Beniko and Theron Shan, two of their closest advisors.
Theron piloted a shuttle to Nathema system, where Lana began feeling the effects of the Force void before even setting foot on the planet. Even Valkorion found his power diminished in this place, though he promised to shield the Alliance Commander and their companion from its worst effects. The shuttle's sensors identified the Sanitarium as the only structure on the planet showing signs of life and Theron dropped off Lana and the Commander not far from it, taking the shuttle to a safe distance afterwards. Meanwhile, Vaylin landed at the entrance to the Sanitarium with a host of the Horizon Guards, where she was greeted by an Abyssin Keeper, who informed Vaylin that Jarak was waiting for her inside his laboratory. The Empress ordered the Horizon Guards to wait outside and ventured in, reaching the habitat in which Jarak kept his twisted experiments. Jarak arrived to witness Vaylin slaughter a trio of his mutated Acklays and informed Vaylin that everything was prepared for her in the main lab, while Lana and the Commander made their way to the entrance of Sanitarium, where they dispatched the Horizon Guards and followed Vaylin inside. Within the walls of the Sanitarium, Lana and the Commander proceeded to cut down skytroopers, Nathema Zealots and Keepers that stood in their way, while learning about Jarak's role in Vaylin's conditioning there from his holorecordings.
In the main laboratory, Jarak had prepared a large circular arena surrounded by massive energy orb nodes and explained to Vaylin that the process to break her conditioning would be even more extreme than before, with nobody else surviving it so far. However, Jarak also assured the Empress that her unparalleled strength in the Force would give her a chance that nobody else had and Vaylin agreed to proceed. The pillar orbs pierced Vaylin's body with energy beams, dealing her enormous pain, and causing her power to lash out of control. As Vaylin struggled, the Force blasts emitted from her body evaporated several Keepers and Zealots, while Jarak had fled the room to save his life. He ran into Lana and the Commander and quickly explained that only he knew a location of a safe place, asking them to escort him there through the beasts that went mad from Vaylin's power. To assure their mutual survival, Jarak led them to the Emperor's Vault in the Sanitarium's lower levels, where they barely managed to get inside to avoid the energy blasts that ravaged everything outside and fried the vault's power circuits. All this time, Vaylin was alone at the mercy of Jarak's inventions and continued to suffer unbearable pain. Finally, determined not to die in the place she hated so much, Vaylin gathered 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 stopped, Vaylin could feel her bonds has 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 Void in the Force that permeated the place. Jarak told the Commander and Lana about the vault's backup power generator, warning them to beware the vault's ancient guardians. After they restored the power, the Commander and Lana made an important discovery by finding Dramath's holocron, which still housed the essence of Valkorion's father killed over 1300 years ago. Dramath told the two the history of his torment and revealed that the holocron held the power to destroy Vitiate once and for all. The Commander ordered Lana to take care of the holocron, since the moment they stepped outside the vault Valkorion would become aware of Commander's actions once again. Jarak was killed by a Vault Guardian and the Commader and Lana had to fight off three large Voreclaws, before finally getting the door of the vault open. Theron informed them that Vaylin has already left the surface and the two rushed to escaped the Sanitarium which now threatened to collapse. The Commander and Lana made their way to the landing platform outside where Theron picked them up, leaving Nathema behind.
The Alliance's original goal ended in failure, with Vaylin succeeding in breaking her chains without even realizing that the Alliance attempted to stop her. Upon the return 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 leave Nathema's orbit. She then immediately ordered the Eternal Fleet to launch an assault on Odessen, intending to finish the Alliance for good. The Alliance, however, managed to locate and obtain Dramath's holocron, a relic that would prove crucial to Vitiate's ultimate destruction, and after learning from Bey'wan Aygo about the attack on Odessen, Theron immediately took the shuttle back to their base. Having sensed her daughter break 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 player has to choose 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 will allow Dramath to join as a temporary companion during Chapter IX: The Eternal Throne, making the fight against Vaylin's spirit much easier.