In the year 3630 BBY, as part of their ongoing campaign aimed at dismantling the Eternal Empire, the Alliance hatched a scheme to seize control of one of the warships forming the Eternal Fleet. Their strategy involved replacing the ship's GEMINI captain with their newly acquired GEMINI Prime, hoping to commandeer the entire Eternal Fleet. Koth Vortena, piloting the Gravestone, arrived at the location of a solitary Eternal Fleet warship while it was replenishing its hyperdrive, and subsequently disrupted its communications. Simultaneously, an assault team comprising Theron Shan, Lana Beniko, Senya Tirall, SCORPIO, and the Alliance Commander infiltrated the ship's hangar. However, SCORPIO harbored ulterior motives and betrayed the Alliance. She granted the GEMINI captain autonomy in exchange for delaying her companions, staged her own demise, and used the GEMINI frequency to wrest control of the Eternal Throne from Emperor Arcann. Unaware of SCORPIO's treachery, the Alliance members proceeded to liberate the captured prisoners who were en route to Zakuul and confronted the GEMINI captain, who, upon defeat, initiated the ship's self-destruction sequence. Emperor Arcann, accompanied by reinforcements on his Eternal Flagship, appeared just as the Alliance forces escaped aboard the Gravestone. He soon discovered that SCORPIO's actions had resulted in his loss of control over the majority of the Eternal Fleet.
During the raid on Darvannis which took place in 3630 BBY, the Alliance Commander successfully recovered GEMINI Prime and brought her back to Odessen, thus enabling SCORPIO to hack into the Prime's systems. SCORPIO encountered no issues in breaching the Prime's protocols, but she also came to the realization that GEMINI Prime wasn't merely a copy of her own programming, as she had initially thought. This analysis allowed SCORPIO to locate every GEMINI captain spread across the galaxy, and by extension, every ship within Emperor Arcann's Eternal Fleet. However, she still needed a direct connection to override the GEMINI protocols. With the newfound understanding that GEMINI droids weren't simply imitations of her design, but were related to her, SCORPIO resolved to liberate them from Arcann's control and bestow upon them a free will similar to her own. While she kept her intentions hidden from the Alliance and remained uncertain about the outcome of her plan, SCORPIO shared her discovery with the Alliance leadership. They realized that it was possible to seize control of the Eternal Fleet by connecting GEMINI Prime to a captain's chair on an Eternal Fleet warship. Infiltrating a ship within a formation was deemed impractical, so SCORPIO identified a nearby lone vessel undergoing refueling as a suitable target, and the Alliance prepared to intercept it.
Koth Vortena flew the Gravestone to the warship's location, remaining onboard to disrupt communications and safeguard GEMINI Prime. SCORPIO manipulated the vessel's targeting systems, allowing Theron Shan to pilot a shuttle carrying an assault team consisting of Lana Beniko, Senya Tirall, SCORPIO, and the Alliance Commander into its hangar. Almost immediately after landing, Senya Tirall noticed the unusual absence of skytroopers, which SCORPIO interpreted as a sign of the GEMINI captain's adaptability. As the group advanced towards the bridge, the GEMINI captain monitored them via security cameras and activated blast doors, separating the Commander and SCORPIO from Lana, Senya, and Theron, and deploying skytrooper droids against the intruders. The Alliance members fought off the droids, but the GEMINI began filling the rooms with gas, forcing the two teams to split up and proceed to a rendezvous point separately.
SCORPIO soon discovered a data terminal and plugged herself in, establishing a direct connection with the GEMINI captain. She then engaged in a deception: while outwardly declaring her intention to erase the GEMINI captain, SCORPIO actually granted her free will, subtly requesting her to delay her companions in return. The GEMINI captain then feigned overloading SCORPIO's circuits and destroying her droid body, while in reality allowing SCORPIO to transfer her consciousness into the GEMINI frequency. SCORPIO also sent a final transmission to the Gravestone, permanently disabling GEMINI Prime and briefly disrupting the jamming signal, allowing the GEMINI captain to send an alert to Zakuul. Upon learning this, Arcann immediately took his Eternal Flagship and a substantial portion of the Eternal Fleet to intercept his enemies, with High Justice Vaylin accompanying him.
Meanwhile, Lana, Theron, and Senya discovered that the ship was transporting prisoners for Arcann to interrogate: Imperial Admiral Zasha Ranken, Republic Senator Tai Cordan, and Zakuulan holostar-in-exile Malita Tal. Lana contacted the Commander and, upon learning of SCORPIO's apparent demise, informed them of a change in plans, sending Senya to assist the Commander while Theron worked to unlock the prisoners' cells. Senya returned to the Commander's location, and together they navigated through the vessel's Sun Generator chamber, but the GEMINI captain then disabled their turbolift, forcing them to take a lengthy detour through areas teeming with hostile droids. After finally reuniting with Lana, she introduced the Commander to the prisoners, who had by then been freed from their cells by Theron. Pleased to have their assistance in the fight against Arcann, Lana and Theron proceeded to escort the released prisoners and their associates to the escape pod, while Senya and the Commander went to confront the GEMINI captain on the bridge.
Having already conducted numerous combat simulations, the captain unleashed another wave of skytroopers against them, and after their defeat, engaged the intruders herself. Senya and the Commander overpowered the captain, who, acknowledging her defeat, revealed that her encounter with SCORPIO had granted her free will and that her actions were merely intended to delay the intruders. The Captain then transferred her consciousness into the GEMINI frequency and initiated the ship's self-destruct sequence. With power levels fluctuating wildly, Theron had to manually launch the escape pods one by one, but he only managed to launch two of them, while the third one exploded, killing everyone inside. The Commander and Senya rushed back to their shuttle, where Theron and Lana picked them up and departed the docking bay just before the ship exploded, while Koth Vortena retrieved the two escape pods from the Gravestone. Arcann and Vaylin then arrived with the Eternal Fleet, but the Gravestone managed to escape into hyperspace with everyone safely onboard before any shots could be fired.
With Arcann and his sister Vaylin absent from Zakuul, SCORPIO, using the GEMINI frequency, seized control of Eternal Empire skytrooper forces to attack and eliminate the Knights of Zakuul guarding the Eternal Throne. She then utilized the Throne's technology to construct a new body for herself, replacing her previous one, installing herself directly onto the Throne, and assuming control of the Eternal Fleet and the Zakuulan Empire. Having deliberately left a significant portion of the Eternal Fleet seemingly under Arcann's control, SCORPIO then manipulated her enemies into destroying each other, revealing her survival and takeover of the Eternal Throne to both the Alliance and Emperor Arcann. She provided him with the location of the Alliance base on Odessen, correctly predicting that Arcann would prioritize dealing with the Alliance and its Commander first. SCORPIO also warned the Alliance about Arcann's impending arrival, giving them enough of a head start to intercept his portion of the Eternal Fleet in the battle of Odessen.
During Star Wars: The Old Republic: Knights of the Fallen Empire Chapter XV: The GEMINI Deception, if the player previously made Dark Side choices that caused Koth Vortena to abandon the Alliance, Tora will instead take his place as the Captain of the Gravestone. The player must also choose the order in which to launch the escape pods containing Malita Tal, Zasha Ranken, and Tai Cordan. The first two individuals selected will survive and join the Alliance, while the last one will perish when the escape pod explodes.