Battle of Odessen

During the Alliance attempt to take over the Eternal Fleet through the use of GEMINI Prime, SCORPIO betrayed the Alliance and through the GEMINI frequency took control of the Eternal Throne herself. She then deliberately left a significant detachment of the Eternal Fleet seemingly under Emperor Arcann's control and manipulated her enemies to destroy each other. She provided Arcann with the location of the Alliance base on Odessen, correctly predicting that Arcann would deal with the Alliance and its Commander first instead of her, and also warned the Alliance about Arcann's imminent arrival, giving them a head-start. The Alliance base and the surrounding area were protected from aerial bombardment by a planetary shield, ensuring that the Eternal Fleet could not wipe the Alliance out with a single devastating attack, but that still left the base vulnerable to walkers and troops. Aric Jorgan volunteered to remain in the base in case of a ground invasion, and Kaliyo Djannis elected to join him, though the Commander assigned one other Alliance member to watch over the two. As Arcann's Eternal Fleet led by his Eternal Flagship jumped in-system, the Alliance leadership boarded the Gravestone to meet them in orbit.

The Eternal Fleet opened fire, which the Gravestone deflector shields absorbed, and Koth Vortena ordered his crew to man the battlestations. Theron Shan went down to the omnicannon, using it to fire the on the Eternal Fleet. Lana Beniko came to conclusion that the only way to ensure Odessen's safety was to destroy Arcann's Eternal Flagship, and decided to board it along with the Commander, Senya Tirall and two more Alliance members, tasked with disabling the flagship's weapons and shields. Theron fired the omnicannon at the Eternal Fleet warship blocking the direct path to the flagship, which also knocked out the flagship's shields long enough to allow the Alliance shuttle to land in its hangar. Upon disembarking, the Alliance forces were attacked by scores of skytroopers, which they managed to fend off.

Sending two teams to disable the shields and guns, Lana and Senya and the Commander proceeded to infiltrate the flagship. At this point, the Gravestone omnicannon stopped working for no discernible reason and Koth send his best engineer Tora to assist Theron. SCORPIO then revealed herself to be behind the malfunction and attempted to remotely take over the Gravestone, but Vortena stopped her by locking the droid out of the ship's systems. After spotting her mother on the security cameras, High Justice Vaylin contacted the group and revealed that Emperor Arcann was on the flagship's bridge, which prompted Senya to separate from the rest and confront her daughter personally. The Commander and Lana fought their way through skytroopers and Knights of Zakuul, defeating the Exarch Shernisa Varless and coming across an experimental assault skytrooper KJ-931.

Koth placed a well-aimed shot on the flagship that hit the droid and allowed Lana and the Commander to gain the upper hand, while the teams send to disable shields and guns likewise accomplished their tasks with relative ease. The Commander and Lana proceeded towards the bridge, defeating the Knight Commander Dara Nadal, at which point Theron noticed and informed Lana that the Eternal Fleet was now targeting the Eternal Flagship, which Lana recognized a part of SCORPIO's ploy 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. The two of them 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.

Demanding Valkorion to address him, Arcann restrained the Commander with the Force and eventually 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 lengthy duel, with Arcann conjuring Force manifestations to assist him, while the Commander picked up a discarded Knight-Captain's shield to block Arcann's attacks. Eventually the Commander managed to overpower Arcann and had him at their mercy, but at this point Eternal Fleet warships opened fire on the flagship, causing multiple fires and serious damage throughout, and crushing Arcann under a pile of falling debris, while the Commander had to retreat to avoid the same 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.

Back on Odessen, Lana congratulated the Commander on their victory, while Kaliyo and Jorgan confirmed that no ground forces ever attempted to land. Arcann was effectively dethroned and following the victory, Imperial and Republic forces have come pouring in to join the Alliance's cause, bringing with them enough starships to form the Alliance fleet. Although Odessen's location was no longer secret, its defenses were formidable enough to ensure the Alliance's safety even against the Eternal Fleet. Apart from Arcann, who was taken by Senya to unknown location, the only other survivor from Zakuulan forces was the High Justice Vaylin, who returned to Zakuul only to find SCORPIO in control of the Eternal Throne. Vaylin cut through SCORPIO's skytrooper defenses, but to her surprise SCORPIO welcomed Vaylin and explained she only took the throne to grant free will to the Fleet's GEMINI captains. Some of the GEMINIs used their newfound freedom to explore the galaxy, taking their warships away from Zakuul, but many decided to stay with SCORPIO, whom they now revered as "Great Mother". Her mission accomplished, SCORPIO willingly surrendered the Eternal Throne to Vaylin, offering to stay and advise the new Empress of Zakuul on how to destroy their enemies.

Early on in Chapter XVI: The Battle of Odessen, player has to assign roles for Vette, Gault Rennow and Torian Cadera, ordering one of them to stay behind 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 end of the battle the player must either make a Light Side option to let Senya and Arcann go, 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 biggest possible difference involves Koth Vortena and his crewmembers Len Parvek and Ralo, who can quit and abandon the Alliance depending on the player's choices during Chapter X: Anarchy in Paradise. In this case, Tora become the captain of the Gravestone instead, though she will still leave the bridge to help Theron Shan with the omnicannon during the battle. Koth will use this opportunity to sneak his way onboard the ship along with his crew and pretend to have forgiven the player, stopping SCORPIO from taking over the Gravestone and firing on the Eternal Flagship to hit KJ-931, claiming that stopping Arcann is all that really matters. However, after Arcann is finished, Koth will reveal that it was just a ploy to steal the Gravestone, as he is worried the player would use it to destroy Zakuul. Putting Theron and Tora in stun cuffs, Vortena ejects them in an escape pod, after which he hijacks the Gravestone and takes it into hyperspace, robbing the Alliance of its best weapon against the Eternal Fleet.