After the Alliance's Commander, famed for leading the war against Zakuul, was falsely declared deceased on Dromund Kaas, the Eternal Empire's Empress, Vaylin, alongside her advisor SCORPIO, initiated a bold attack against the Gravestone. This vessel was the sole Alliance warship capable of challenging their formidable Eternal Fleet. They seized the Ridala, a civilian cargo freighter, murdering its captain and simulating an assault. When Koth Vortena, piloting the Gravestone, arrived to engage the Eternal Fleet, SCORPIO cleverly posed as the freighter's captain, sending out a false distress signal. Vortena, deceived, permitted the Ridala to dock within the Gravestone's hangar for purported repairs. From this concealed position, SCORPIO, Vaylin, and a contingent of Knights of Zakuul and Horizon Guard swiftly subdued Koth's crew, seizing control of the warship. Vortena, however, evaded capture and desperately contacted the Alliance for assistance. The Alliance responded by deploying their fleet to confront the Eternal Fleet warship, while the Alliance Commander and Lana Beniko stealthily infiltrated the Gravestone using a boarding pod. Once aboard, they neutralized several skytrooper patrols as they made their way to Vortena. Koth then revealed to them that Vaylin's forces were at risk of setting off the quantum bomb that he had strategically installed as a safeguard against SCORPIO. The Commander joined him in the task of deactivating the bomb's fuses, while Beniko created a diversion. SCORPIO detected the presence of the quantum bomb and, determined to preserve the warship at all costs, orchestrated the departure of Vaylin and her Horizon Guard from the bridge, allowing the Alliance Commander and Vortena to reclaim it. She then informed them that Lana Beniko was trapped by Vaylin within the Dark Sanctuary and needed immediate assistance. The Commander and Vortena arrived just in time to rescue Beniko. As the Commander engaged Vaylin, who was preparing to strike a fatal blow, Valkorion intervened, triggering her secret conditioning, rendering her unable to attack. Powerless to fight, Vaylin turned and fled, granting Vortena the opportunity to disarm the bomb. Just as Theron Shan arrived with reinforcements, landing an Alliance shuttle within the hangar, SCORPIO seized control of the Gravestone, setting course for a destination she had discovered within the ship's subroutines. The warship then jumped out of hyperspace in the Iokath system, finding itself surrounded by the entire Eternal Fleet. ARIES, the droid overseeing Iokath, then unleashed a superweapon that emitted a blinding light, rendering all organic beings aboard the ships unconscious, and subsequently arranging them across the surface of Iokath for combat simulations.
Shortly following the Invasion of Voss, reports emerged from Dromund Kaas indicating the death of the Alliance's Commander. This information, however, was a fabrication, part of a scheme orchestrated by former Republic Supreme Chancellor Leontyne Saresh and Imperial Minister of Logistics Gelmid Lorman to seize control of both the Empire and the Alliance by simultaneously assassinating their leaders. SCORPIO conveyed this news to the Eternal Empire's Empress Vaylin, who quickly discerned the falsehood of the rumors, sensing that her father's spirit remained within the Commander's mind. Nevertheless, SCORPIO emphasized that the truth was irrelevant, and the resulting chaos presented an ideal opportunity to strike against the Alliance. With the Gravestone as her primary objective, SCORPIO and Vaylin devised a trap for the only warship capable of challenging their Eternal Fleet. They captured a civilian cargo freighter called the Ridala, murdering its captain and staging a simulated attack by the Eternal Fleet.
Vaylin, SCORPIO, and a number of Knights of Zakuul boarded the freighter, which was then subjected to simulated fire from the Eternal Fleet warships. SCORPIO, impersonating the ship's captain, transmitted a distress call, which was eventually answered by Koth Vortena, the captain of the Gravestone. Vortena, deceived, allowed the Ridala to dock within the Gravestone's hangar for emergency repairs. This enabled Vaylin's forces to subdue Koth's crew and seize control of the warship. Vortena himself managed to evade capture and contacted the Alliance base on Odessen for assistance, successfully transmitting his coordinates before the transmission was cut off. SCORPIO was unable to gain complete control of the ship's systems because Vortena had previously locked the bridge controls, preventing her from accessing essential systems such as shields, weapons, and the hyperdrive.
The Alliance fleet emerged from hyperspace and engaged the Eternal Fleet, but this was merely a diversion to allow Lana Beniko and the Alliance Commander to board the Gravestone using a boarding pod. Unable to access the HoloNet signal due to the ongoing battle, SCORPIO instructed Vaylin to torture the crewmembers to obtain Vortena's personal details, which could help break his personal encryption key. Meanwhile, Beniko and the Commander neutralized several skytrooper patrols and met with Koth, who revealed that unlocking the primary passcode without entering a second hidden one would trigger the quantum bomb installed as a precaution against SCORPIO. The Commander joined Koth in deactivating the fuses scattered throughout the ship, while Lana diverted Vaylin's forces. Upon learning that the encryption key was based on the list of soldiers who had died under Koth's command during his war service, SCORPIO unlocked his primary key, while also discovering a second password.
Determined to save the Gravestone at any cost, SCORPIO maneuvered Vaylin and her Knights to leave the bridge, pointing out that five patrols at opposite ends of the ship had been lost and revealing that Vortena was receiving assistance from the Commander. Vaylin departed to confront her father, who resided within the Commander's mind, leaving the bridge and Vortena's crewmembers unguarded. Koth and the Commander deactivated the fuses on the first deck, and after eliminating Horizon Guard Tragus Rova, they proceeded towards the bridge, surprised to find it devoid of Vaylin's forces. Vortena deactivated the quantum bomb from the bridge console and instructed Len Parvek, Tora, and the rest of his crew to evacuate in the escape pods. SCORPIO then contacted the bridge, revealing that she had allowed them to reach the bridge so that Vortena could deactivate the bomb, and also informing them that Lana Beniko was trapped by Vaylin in the Dark Sanctuary, where the bomb was hidden.
The Commander and Vortena engaged and defeated Vella Zarkot and reached the Sanctuary just in time to save Beniko from Vaylin's lightsaber. However, their fighting still triggered the bomb, leaving only three minutes until detonation. Vaylin Force-pushed Lana aside and engaged the Commander, quickly gaining the upper hand and preparing to deliver a fatal blow. However, the spirit of Valkorion himself intervened to protect his host and stopped time in his vicinity, but Vaylin was able to break through and regain her freedom of movement. Engaging in a conversation with her father for the first time since his physical death, Vaylin blamed him for imprisoning her on Nathema, while Valkorion insisted that his actions were intended to keep her safe. Vaylin then prepared to strike the Commander when Valkorion uttered the phrase "Kneel before the Dragon of Zakuul," triggering her secret mental conditioning and rendering her powerless.
Unable to retaliate, Vaylin became enraged and confused, fleeing the Dark Sanctuary and giving Vortena the opportunity to disarm the quantum bomb, while the Commander disabled the power relays to prevent its premature detonation. As these events unfolded in the Dark Sanctuary, SCORPIO finally gained unrestricted access to the Gravestone, uncovering hidden files and subroutines dating back thousands of years, revealing the place of origin of herself, the Gravestone, and the Eternal Fleet. Utilizing her connection to the GEMINI droids, SCORPIO instructed them to travel to those coordinates, ending the space battle and leaving only the Alliance ships in the vicinity of the Gravestone. Theron Shan brought Kaliyo Djannis, Aric Jorgan, Torian Cadera, and Vette as reinforcements, landing an Alliance shuttle inside the Gravestone hangar just moments before SCORPIO announced that she was taking control of the Gravestone and urged the organic beings to abandon ship.
Realizing that she had been betrayed, Vaylin confronted SCORPIO on the bridge and attempted to attack her, but SCORPIO engaged and locked the vessel's hyperdrive, setting course for the same destination to which she had sent the Eternal Fleet. Both Vaylin and SCORPIO then left the bridge, where the Alliance forces converged and witnessed the Gravestone jumping out of hyperspace in the Iokath system, surrounded by the entirety of the Eternal Fleet. SCORPIO departed the ship in the shuttle Ridala and contacted the Alliance again, revealing that Vaylin and her remaining forces were sabotaging everything they could on the Gravestone. Koth Vortena and the Commander rushed to the omnicannon, but in their absence, Vaylin returned to the bridge and overpowered both Kaliyo and Aric Jorgan. She threatened to kill Torian and Vette but was unable to harm anyone before a blinding white light emanating from Iokath engulfed the ship.
The Gravestone and the Eternal Fleet were transported to Iokath, a massive sphere constructed around a star by a long-dead species and controlled by a self-aware droid known as ARIES. As the vessels approached and entered Iokath, ARIES activated a superweapon that emitted a blinding light, rendering all organic beings aboard the ships unconscious. He then arranged and positioned them across the surface of Iokath to test them in various combat scenarios, isolating Vaylin and SCORPIO as the most dangerous individuals. Both the Alliance and Eternal Empire forces from the Eternal Fleet warships then worked to regroup and reclaim their ships from ARIES so that they could escape from Iokath.
Knights of the Eternal Throne Chapter III: Dark Reunions unfolds differently if the player's previous Dark Side choices led Koth Vortena to abandon the Alliance and subsequently steal the Gravestone. In this scenario, Tora remains loyal to the Alliance and is not present when Vaylin's forces capture Koth's crew. Requiring external assistance to deactivate his quantum bomb, Koth reluctantly contacts the Alliance for help despite their mutual animosity. After the quantum bomb is deactivated, the player has the option to either kill Koth on the spot for his betrayal or spare his life, in which case Vortena will be captured on Iokath along with the rest, but will still leave the Alliance afterward.