Battle of Zakuul

Following the death of Eternal Empress Vaylin during the assault on Odessen, the remaining forces of the Eternal Empire on Odessen surrendered to the Alliance, bringing the ground battle to an end. However, Vaylin's demise also left the Eternal Throne vacant, causing the Eternal Fleet's GEMINI captains to become rogue and revert to their most fundamental programming: the extermination of all complex life forms in the galaxy. Eternal Fleet warships departed from Odessen's orbit and initiated bombardments on densely populated worlds, including Dromund Kaas, Coruscant and the other Core Worlds, and Zakuul itself. Furthermore, the Eternal Fleet established a blockade around Zakuul, destroying any vessels attempting to land or take off, thereby safeguarding the Eternal Throne within a ray shield, while also unleashing fire upon the Spire itself, resulting in the collapse of entire buildings and the presence of corpses in the streets.

The populace of Zakuul had not yet been informed of the Empress's death. Some speculated that she had ordered the slaughter, while others correctly surmised that Vaylin was dead and the Eternal Fleet had gone haywire. However, Vaylin was not entirely gone; at the moment of her physical death, Valkorion absorbed her spirit into the Alliance Commander's body, which he already occupied, thereby granting the Immortal Emperor the means to overcome his host's mental defenses. Meanwhile, recognizing that claiming the Eternal Throne was the only way to halt the destruction, the entire Alliance leadership boarded the Gravestone and set course for Zakuul. The Commander also instructed Lana Beniko to bring Dramath's holocron, which they had recovered on Nathema and hoped to use as a weapon against Valkorion.

Protected by the Alliance fleet, the Gravestone emerged from hyperspace in Zakuul's orbit, which was completely blockaded by Eternal Fleet warships. Nevertheless, the Gravestone possessed an advantage in the form of upgrades based on schematics acquired on Iokath, which enhanced the vessel's shields, enabling it to withstand concentrated fire from the Eternal Fleet and breach the blockade. Subsequently, the Gravestone began firing its omnicannon, destroying multiple warships with each blast. The Alliance Commander prepared to descend to the surface, and former Emperor Arcann and his mother Senya Tirall volunteered to accompany them in an escape pod, which they used to land in the Garden of Izax amidst the surrounding fire and destruction.

They proceeded towards the Spire, engaging skytroopers and Knights of Zakuul along the way, who were still unaware of the Empress's death. At the entrance to the Eternal Throne Spire, the Knights obstructed their path with a Tyth's Gauntlet, but Indo Zal and Zakuulan rebels unexpectedly arrived to provide assistance, destroying an Eternal Empire Walker with a rocket launder. After battling through waves of security, the Commander, Senya, and Arcann eventually reached the turbolift that led directly to the Eternal Throne. Upon entering the room for the first time in nearly a year, Arcann was taken aback by the sight of his former Throne and, feeling compelled to atone for his past misdeeds, offered it to the Commander, declaring them a more deserving Emperor than he had ever been. The Commander ascended the Throne, which sent a jolt through their body and transmitted a signal to the Eternal Fleet, causing it to immediately cease fire across the galaxy, averting potentially catastrophic casualties.

However, as soon as the Commander occupied the Eternal Throne, Valkorion betrayed them and revealed his true objective, forcing the Commander to kneel and expressing his desire to eradicate the Commander's mind and seize their body, after which he shocked them into oblivion. At that moment, attacking skytroopers breached the Throne room, compelling Senya and Arcann to defend their position before they could offer assistance. The Commander awoke within the abyss of their own psyche, subconsciously assuming Valkorion's form in an attempt to prevent their identity from being completely erased. While traversing the bizarre mindscape, the Commander cleansed their corrupted memories, which revealed the thoughts and motivations Valkorion had while inhabiting their body. Upon locating a mental representation of the Holocron, the Commander regained their identity, causing Valkorion to manifest in his usual form, intending to complete the task of destroying his vessel's consciousness.

The Commander resisted, and Valkorion summoned Vaylin's enslaved spirit, dominating her will and ordering his daughter to destroy the Outlander. The Commander battled Vaylin in the mental mindscape and emerged victorious, but Valkorion easily restored her spirit. Subsequently, the Commander used the representation of the holocron to free Vaylin from her father's mind control. At this point, Arcann joined them inside the Commander's mind by meditating at the physical holocron still located in the Throne room. The Commander and Arcann convinced Vaylin to join them against Valkorion, and the three of them attacked the Immortal Emperor. After toying with them for a while, Valkorion destroyed the holocron, claiming that nothing could stop him. However, because his spirit was now bound to Vaylin's and shared her weakness, the Commander exploited Vaylin's mental conditioning to turn the tables on Valkorion and rob the Emperor of his own strength. With Valkorion overpowered and weakened, Senya joined her children in the Commander's mind, and together the family witnessed the Immortal Emperor's final words and moments, until the Commander brought a definitive end to his millennia-long existence.

Following the destruction of Valkorion's essence, the Commander, Senya, and Arcann found themselves back in the Eternal Throne room, where Arcann was able to confirm that he no longer sensed his father's presence, who was gone for good. Senya then activated a system-wide holochannel for the new owner of the Eternal Throne, who delivered an address to the galaxy and proclaimed the dawn of the Eternal Alliance. In the ensuing days, the Alliance established complete control over the Eternal Fleet and the remnants of the Zakuulan military force, appropriating its vehicles and recruiting personnel for the armed forces of the new Eternal Alliance, which had evolved from a small-scale insurrection into one of the major galactic powers alongside the Galactic Republic and the Sith Empire. While the other governments were occupied with recovery efforts on the worlds that had suffered from the Eternal Fleet's bombardment, both were soon preparing for a renewed large-scale war, which had been put on hold since the Eternal Empire conquest. The Eternal Alliance relocated the Eternal Throne from the Spire to Odessen, where it was installed in the Alliance base, allowing the Commander to issue new orders directly to the Eternal Fleet.

Several aspects of "Chapter IX: The Eternal Throne" can unfold in different ways, depending on the player's past choices. Either Vette or Torian Cadera is killed by Vaylin on Odessen during "Chapter VIII: End Times," and the player must choose which one to save; the survivor will appear on the Gravestone before the battle and during the Eternal Alliance celebration at the very end. Similarly, either Aric Jorgan or Kaliyo Djannis can be killed or exiled by the player during Knights of the Fallen Empire "Chapter XIII: Profit and Plunder," in which case they will not appear during the battle. If the player previously killed or exiled Koth Vortena, Hylo Visz will replace him as the captain of the Gravestone, piloting the vessel and using the upgraded shields to breach the blockade around Zakuul.

If the player previously killed Arcann and Senya Tirall, Theron Shan and Lana Beniko will accompany them to the Eternal Throne room instead, although the spirits of Arcann and Senya will still appear to help the player defeat Valkorion. If, during "Chapter VI: The Dragon's Maw," the player ordered Indo Zal to lead the Zakuulan rebels into battle instead of taking them to safety, Indo will still appear to provide assistance, but will mention that the rebels have lost faith in the Alliance. If Arcann was killed without achieving redemption, both his and Vaylin's spirits will be absorbed by Valkorion and ordered to attack the player, who will free them with Dramath's holocron and convince them to join their side, despite having killed them both. If, during "Chapter VII: Into the Void," the player has kept Lord Dramath imprisoned in his holocron, his spirit will appear to assist the player, confronting his son, killer, and tormentor. After defeating Vaylin's spirit, Dramath will attack Vitiate, piercing his defense at the cost of his life, finally achieving oblivion after centuries spent between life and death.

If previously killed on Voss, Senya will still appear in the player's mind to help finish Valkorion, though her lines and actions will be exactly the same as in the outcome where she remains alive and enters the player's mind via holocron. After Valkorion is defeated, the player can address the galaxy as a peacekeeper in a Light Side option or as a new Emperor in a Dark Side option. In the Light Side option, the people of Zakuul are left free to govern themselves, and the Eternal Fleet is transformed into a peaceful armada delivering refugees and supplies to help the galaxy rebuild after the war. In the Dark Side option, Zakuul explicitly surrenders to Alliance control, with Valkorion's name expressly forbidden from being spoken again, while the Eternal Fleet is used as a deterrent to prevent the other galactic powers from challenging the Eternal Alliance. This choice affects several lines and cutscenes during subsequent events on Iokath and Umbara.