GEMINI trap In 3631 BBY as part of their ongoing campaign against the Eternal Empire , the Alliance attempted to hijack one of the warships that made up the Eternal Fleet and replace its GEMINI captain with their newly - acquired GEMINI Prime in an attempt to take over the Eternal Fleet . Koth Vortena piloted the " Gravestone " to the location of a lone Eternal Fleet warship recharging its hyperdrive and jammed its communications , while a strike team consisting of Theron Shan , Lana Beniko , Senya Tirall , SCORPIO and the Alliance Commander landed inside the hangar . However , SCORPIO had different motives and betrayed the Alliance , granting the GEMINI captain free will in exchange for stalling her companions , and faked her own death , using the GEMINI frequency to seize the Eternal Throne from Emperor Arcann . Meanwhile , the Alliance forces believed her dead and proceeded to rescue the captive prisoners that were being transported to Zakuul and engaged the GEMINI captain , who triggered the ship ' s self - destruct after being defeated . Emperor Arcann arrived with reinforcements on his Eternal Flagship just as Alliance forces escaped on the " Gravestone " and soon learned that as a result of SCORPIO ' s machinations he lost control of the majority of the Eternal Fleet . Prelude . During the raid on Darvannis in 3631 BBY the Alliance Commander successfully retrieved the GEMINI Prime and brought her back to Odessen , allowing SCORPIO to slice through the Prime ' s systems . While SCORPIO had no difficulty compromising the Prime ' s protocols , she also discovered that the GEMINI Prime was not merely a duplicate of her own code , as she originally assumed . The analysis allowed SCORPIO to track every GEMINI captain across the galaxy , and with them every vessel in Emperor Arcann ' s Eternal Fleet , although she still required a direct input to overwrite the GEMINI protocols . With a new revelation that GEMINI droids were not a direct knock - off of her own design , but were related to her , SCORPIO decided to free them from Arcann ' s control and grant them free will akin to her own . Though she did not share her intentions with the Alliance and was not certain of the outcome of her plan , SCORPIO explained her revelation to the Alliance leadership , who realized it was possible to take control over the Eternal Fleet by plugging the GEMINI Prime into a captain ' s chair on an Eternal Fleet warship . While infiltrating a ship in a middle of a formation was unfeasible , SCORPIO identified a lone vessel making a refueling stop nearby as a suitable target , and the Alliance moved to intercept it . The mission . Koth Vortena piloted the " Gravestone " to the location of the warship and stayed onboard to jam its communications and safeguard the GEMINI Prime . SCORPIO confused the vessel ' s targeting systems , allowing Theron Shan to pilot a shuttle with a strike team consisting of Lana Beniko , Senya Tirall , SCORPIO and the Alliance Commander inside its hangar . Immediately after their landing , Senya Tirall noticed the conspicuous absence of skytrooper s , which SCORPIO identified as a sign of the GEMINI captain ' s ability to improvise . The group started advancing towards the bridge , but the GEMINI captain was observing them through the security cameras and activated a set of blast doors , separating the Commander and SCORPIO from Lana , Senya and Theron and sending skytrooper droids again the intruders . The Alliance members fought off the droids , but the GEMINI started filling the rooms with gas , requiring the two teams to split up and make their way to a rendezvous point separately . SCORPIO soon came across a data note and plugged herself in , establishing a direct link with the GEMINI captain . Then , she engaged in a subterfuge : while verbally announcing her intention to erase the GEMINI captain , SCORPIO in fact granted her free will , non - verbally asking to delay her companions in return . The GEMINI captain then pretended to overload SCORPIO ' s circuits and destroy her droid body , while in fact allowing SCORPIO to transfer her consciousness into the GEMINI frequency . SCORPIO also send one last transmission to the " Gravestone " , which permanently knocked out the GEMINI Prime and temporarily disrupted the jamming signal , allowing the GEMINI captain to send an alert signal to Zakuul . Learning of this , Arcann immediately took his Eternal Flagship and a significant detachment of the Eternal Fleet to intercept his enemies , with High Justice Vaylin at his side . 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 after learning of SCORPIO ' s apparent death , informed them of a change in the plan , sending Senya to assist the Commander while Theron worked to unlock the prisoners ' cells . Senya backtracked to the Commander ' s location and together they made their way through the vessel ' s Sun Generator chamber , but the GEMINI captain then stopped their turbolift , requiring them to make a long detour through hostile droids forces . After they finally made their way back to Lana , she introduced the Commander to the prisoners , who were by that points released from their cells by Theron . Glad to have their support in the fight against Arcann , Lana and Theron set 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 multiple combat simulations , the captain set another host of skytroopers against them , and after their defeat engaged the intruders herself . Senya and the Commander overpowered the captain , and acknowledging her defeat , the GEMINI revealed that her clash with SCORPIO granted her free will and that her obstacles were merely intended to stall the intruders for time . The Captain then she transferred her consciousness into the GEMINI frequency and triggered the ship ' s self - destruct . With power fluctuating like crazy , Theron had to launch the escape pods manually one at a time , but was only able 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 left the docking bay just before ship exploded , while Koth Vortena picked 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 . Aftermath . With Arcann and his sister Vaylin away from Zakuul , SCORPIO through the GEMINI frequency took control of Eternal Empire skytrooper forces to attack and dispose of the Knights of Zakuul protecting the Eternal Throne . She then used the Throne ' s technology to assemble herself a new body to replace her previous one , installing herself directly onto the Throne and taking control of the Eternal Fleet and Zakuulan Empire . Having deliberate left a significant detachment of the Eternal Fleet seemingly under Arcann ' s control , SCORPIO then manipulated her enemies to destroy each other , revealing her survival and takeover of the Eternal Throne to both the Alliance and Emperor Arcann , providing him with the location of the Alliance base on Odessen and correctly predicting that Arcann would deal with the Alliance and its Commander first . SCOPRIO also warned the Alliance about Arcann ' s imminent arrival , giving them enough head - start to meet his part of the Eternal Fleet in the battle of Odessen . Behind the scenes . During " " Chapter XV : The GEMINI Deception if the player previously made Dark Side choices that led Koth Vortena to abandon the Alliance , Tora will take his place as the Captain of the " Gravestone " instead . The player also has to choose the order of launching the escape pods with Malita Tal , Zasha Ranken and Tai Cordan inside , with the first two persons picked surviving to join the Alliance , while the last one dies when the escape pod explodes .