Shortly into the Galactic Empire's rule, Imperial spies locate a Jedi survivor of the Great Purge named Kento Marek on Kashyyyk. Darth Vader arrives and defeats Marek in battle,[17][18] shortly before Marek's son Galen grabs Vader's lightsaber with the Force. Realizing the boy's strong connection to the Force, Vader kills Marek and leaves with Galen, raising him to become his apprentice in secret.
Years later, an adult Galen (given the alias "Starkiller") completes his training. He is sent by Vader to eliminate several Jedi survivors across the galaxy in preparation for assassinating the Emperor so that the two of them can rule the galaxy together. Starkiller travels aboard his personal ship, the Rogue Shadow, alongside training droid PROXY (who is programmed to try and kill Starkiller) and Imperial pilot Juno Eclipse.[19] Starkiller's targets include Rahm Kota, a Clone Wars veteran and leader of a militia;[d] Kazdan Paratus, insane after years of isolation on Raxus Prime;[e] and Shaak Ti, who is hiding on Felucia. Before she dies, Shaak Ti warns Starkiller that he will eventually be betrayed by Vader. His final mission complete, Starkiller is summoned by Vader as the Emperor arrives. Vader then swiftly impales Starkiller, and at the Emperor's insistence, hurls his apprentice through a window into space to prove his loyalty.
Unbeknownst to the Emperor, Vader has Starkiller recovered and resuscitated. Vader sends Starkiller to foster a rebellion among the Empire's enemies, as part of his plan to create the proper conditions to overthrow the Emperor. Starkiller rescues Juno, who had been arrested and branded a traitor to the Empire, and escapes with her and PROXY. Looking for allies to aid his mission, Starkiller finds an alive Kota on Cloud City, rendered blind and reduced to alcoholism, and rescues him from Imperial forces.
The group travels to Kashyyyk to locate Kota's contact, senator Bail Organa. Starkiller discovers his old home and meets his father's spirit, who expresses remorse for Starkiller's upbringing under Vader.[f] To gain Bail's trust, Starkiller rescues his captive daughter Princess Leia Organa, and liberates the enslaved Wookiees at her request. Starkiller learns from Kota that Bail went missing on Felucia, after searching for Shaak Ti in the hope she would rescue Leia. Starkiller travels to Felucia to find Bail, discovering he had been captured by Shaak Ti's former apprentice Maris Brood, who succumbed to the Dark Side after her master's death. Starkiller defeats Brood but spares her life, and convinces Bail to join the rebellion.
To convince more dissidents to do the same, Vader suggests that Starkiller attack a Star Destroyer facility on Raxus Prime to show that the Empire is vulnerable. Juno learns Starkiller is still serving Vader and chastises him, but agrees to keep silent. On Raxus Prime, Starkiller is attacked by PROXY, who attempts to fulfill his programming by killing him, but Starkiller defeats him, destroys the facility, and pulls a falling Star Destroyer out of the sky using the Force.[g] Bail meets with fellow senators Mon Mothma and Garm Bel Iblis on Corellia to formally organize a rebellion, only for Vader to arrive and arrest them and Kota. After overpowering Starkiller, Vader reveals that he was merely a tool to lure out the Empire's enemies, and had never intended to use him to overthrow the Emperor. Starkiller escapes after PROXY sacrifices himself by attacking Vader.
Juno rescues Starkiller, who uses the Force to see that Kota and the senators are being held on the Death Star. After bidding farewell to Juno, Starkiller battles his way through the station to reach the Emperor's throne room. Vader confronts him, but Starkiller defeats his former master and faces the Emperor, who tries to goad him into killing Vader so Starkiller can take his place. Kota tries to attack the Emperor, but is subdued with Force lightning. At this point, the player must choose between saving Kota (Light Side) or killing Vader (Dark Side).