Battle of Odessen

During the Alliance's attempt to seize the Eternal Fleet using GEMINI Prime, SCORPIO betrayed the Alliance, employing the GEMINI frequency to assume control of the Eternal Throne. She strategically left a significant portion of the Eternal Fleet seemingly under the command of Emperor Arcann, manipulating her enemies into self-destruction. She provided Arcann with the coordinates of the Alliance base on Odessen, correctly anticipating that Arcann would prioritize dealing with the Alliance and its Commander over her. Simultaneously, she alerted the Alliance to Arcann's imminent arrival, granting them a crucial advantage. A planetary shield protected the Alliance base and its surroundings from aerial bombardment, preventing the Eternal Fleet from wiping out the Alliance with a single, devastating strike. However, the base remained vulnerable to ground assaults by walkers and troops. Aric Jorgan volunteered to remain at the base in anticipation of a ground invasion, and Kaliyo Djannis chose to join him, although the Commander assigned another Alliance member to oversee them. As Arcann's Eternal Fleet, led by his Eternal Flagship, entered the system, the Alliance leadership boarded the Gravestone to confront them in orbit.

The Eternal Fleet initiated the attack, with the Gravestone's deflector shields absorbing the initial barrage. Koth Vortena instructed his crew to take their positions at the battlestations. Theron Shan descended to the omnicannon, utilizing it to fire upon the Eternal Fleet. Lana Beniko reached the conclusion that the only way to guarantee Odessen's safety was to eliminate Arcann's Eternal Flagship. She decided to board it, accompanied by the Commander, Senya Tirall, and two additional Alliance members tasked with disabling the flagship's weapons and shields. Theron discharged the omnicannon at the Eternal Fleet warship obstructing the direct path to the flagship, simultaneously disabling the flagship's shields long enough for the Alliance shuttle to land in its hangar. Upon disembarking, the Alliance forces were ambushed by numerous skytroopers, whom they successfully repelled.

Dispatching two teams to deactivate the shields and guns, Lana, Senya, and the Commander proceeded to infiltrate the flagship. At this juncture, the Gravestone omnicannon ceased functioning for an inexplicable reason, prompting Koth to dispatch his top engineer, Tora, to assist Theron. SCORPIO then revealed her involvement in the malfunction and attempted to remotely seize control of the Gravestone, but Vortena thwarted her by locking the droid out of the ship's systems. After identifying her mother on the security cameras, High Justice Vaylin contacted the group, revealing that Emperor Arcann was on the flagship's bridge. This prompted Senya to separate from the others and confront her daughter directly. The Commander and Lana fought their way through skytroopers and Knights of Zakuul, defeating the Exarch Shernisa Varless and encountering an experimental assault skytrooper, KJ-931.

Koth executed a precise shot on the flagship, striking the droid and enabling Lana and the Commander to gain the upper hand. Simultaneously, the teams deployed to disable the shields and guns successfully completed their missions with relative ease. The Commander and Lana advanced towards the bridge, defeating the Knight Commander Dara Nadal. At that point, Theron observed and informed Lana that the Eternal Fleet was now targeting the Eternal Flagship, which Lana recognized as part of SCORPIO's scheme to eliminate both Arcann and the Commander in one fell swoop. The two of them then reached the bridge, but were pursued by four Zakuulan Knights, which Lana stayed behind to deal with, leader the Commander to confront Arcann alone. Alone on the bridge, Arcann explained to the Commander that his animosity was never directed against them personally, but rather against his father Valkorion, whose spirit not existed within the Commander's mind.

Arcann, demanding Valkorion to address him, restrained the Commander with the Force and ultimately struck them with his lightsaber, an attack that was unconsciously blocked by the Commander due to Valkorion's presence. The two then engaged in a prolonged duel, with Arcann summoning Force manifestations to aid him, while the Commander seized a discarded Knight-Captain's shield to deflect Arcann's attacks. Eventually, the Commander overpowered Arcann and had him at their mercy. However, at that moment, Eternal Fleet warships opened fire on the flagship, causing widespread fires and significant damage, crushing Arcann beneath a pile of falling debris, while the Commander had to retreat to avoid a similar fate.

Learning from Theron that the omnicannon was back online and from Lana that the rest of their infiltration team sans Senya was already at their escape shuttle, the Commander took Lana's suggestion to board a small patrol craft nearby rather than run all the way back to the shuttle as the ship was falling apart. Meanwhile Senya reached the bridge and used telekinesis to clear the debris and pull her son from under it, wounded from the fight and with his cybernetics damaged. Vaylin then returned to the burning bridge, mocking her mother for being too late to save Arcann and calling her weak for leaving her children behind. Senya offered both her children to come back to her, but Vaylin angrily refused and launched herself at her mother, only for Arcann to Force-push her away.

Enraged at her brother, Vaylin demanded to know why he saved Senya's life, but before he could answer, falling debris forced Vaylin to retreat and flee back to Zakuul, while Senya took her wounded son to his personal shuttle. Commandeering a small Zakuulan craft, the Commander escaped the burning flagship and contacted the Alliance for status updates, at which point Senya revealed that she was alive and taking Arcann away in hopes of redeeming him. Koth Vortena pleaded the Commander to shoot her shuttle down, but the Commander relented, allowing Senya and Arcann to escape. Theron Shan then fired one last omnicannon shot on the Eternal Flagship, creating a massive chain explosion that completely wiped out the present portion of the Eternal Fleet, winning the battle for the Alliance, who did not suffer a single casualty.

Upon returning to Odessen, Lana congratulated the Commander on their triumph, while Kaliyo and Jorgan confirmed that no ground forces had attempted to land. Arcann was effectively removed from power, and following the victory, forces from the Imperial and Republic factions flocked to join the Alliance's cause, providing enough starships to establish the Alliance fleet. Although Odessen's location was now compromised, its defenses were sufficiently robust to ensure the Alliance's safety, even against the Eternal Fleet. Aside from Arcann, who was taken by Senya to an undisclosed location, the sole surviving member of the Zakuulan forces was High Justice Vaylin, who returned to Zakuul only to discover SCORPIO in control of the Eternal Throne. Vaylin breached SCORPIO's skytrooper defenses, but to her astonishment, SCORPIO welcomed Vaylin and explained that she had only seized the throne to grant free will to the Fleet's GEMINI captains. Some of the GEMINIs utilized their newfound freedom to explore the galaxy, taking their warships away from Zakuul, but many chose to remain with SCORPIO, whom they now revered as "Great Mother." Having accomplished her objective, SCORPIO willingly relinquished the Eternal Throne to Vaylin, offering to stay and advise the new Empress of Zakuul on strategies to destroy their enemies.

Early in Chapter XVI: The Battle of Odessen, the player must assign roles to Vette, Gault Rennow, and Torian Cadera, instructing one of them to remain on Odessen. If players have initiated a romance with any one of their present companions prior or during Knights of the Fallen Empire, the two of them will share a moment on either on Odessen or on the Gravestone. Once the Outlander proceeds to the hanger, they will have to assign one of the three companions listed above to sabotage the weapons on the Eternal Flagship, and the last one to sabotage the flagship's shields. In any case, shields and guns are disabled successfully and the ground forces never land on Odessen, the only difference being in dialogue. On the flagship, the player must choose to receive assistance from either Zakuulan weapons and armor or defensive turrets; this choice only affects the gameplay and has no effect on the story. During the duel against Arcann the player can use a special weapon constructed during Chapter XII: Visions in the Dark to receive two additional special abilities; this is not reflected in dialogue and is not required to defeat Arcann. The player can take a Dark Side option named [Kill Arcann] at the end of the duel, but Arcann will survive and be crushed by debris regardless.

At the conclusion of the battle, the player must either make a Light Side decision to allow Senya and Arcann to depart or a Dark Side choice to open fire on their shuttle. Although they will escape into hyperspace regardless, the choice only affecting some lines in the Knights of the Eternal Throne, dialogue remaining in the game files indicates that at some point the second option actually led to the shuttle being shot down and burning in Odessen's atmosphere, with both Senya and Arcann dead. Arcann's fate remains the same in the finished version, though other events surrounding the battle may change depending on previous Dark Side choices made by player. Either Kaliyo or Jorgan can be killed or permanently exiled at the end of Chapter XIII: Profit and Plunder, in which case different reason will be given for requiring someone else to stay alongside the remaining person.

The most significant potential divergence involves Koth Vortena and his crewmembers Len Parvek and Ralo, who may resign and abandon the Alliance depending on the player's choices during Chapter X: Anarchy in Paradise. In this scenario, Tora assumes the role of captain of the Gravestone instead, although she will still leave the bridge to assist Theron Shan with the omnicannon during the battle. Koth will exploit this opportunity to stealthily board the ship with his crew and feign forgiveness, preventing SCORPIO from seizing control of the Gravestone and firing on the Eternal Flagship to strike KJ-931, asserting that stopping Arcann is the paramount objective. However, after Arcann is defeated, Koth will reveal that this was merely a ruse to steal the Gravestone, as he fears the player will use it to destroy Zakuul. Restraining Theron and Tora with stun cuffs, Vortena ejects them in an escape pod, subsequently hijacking the Gravestone and taking it into hyperspace, depriving the Alliance of its most potent weapon against the Eternal Fleet.