The war itself had been orchestrated by the Dark Lord of the Sith Darth Sidious, who turned the clone army against the Jedi through his public guise as Supreme Chancellor Palpatine, shortly before his ascension as Emperor of the galaxy.
As a result, they reluctantly deserted the Order and fled to the Outer Rim Territories prior to Order 66, a contingency directive that instructed all Republic clone troopers to execute their Jedi officers-the culmination of a Sith plot to exterminate their ancient rivals while simultaneously transforming the Republic into a dictatorship.
His parents were both members of the Jedi Order they married in secret during the Clone Wars, a conflict between the Galactic Republic and the Confederacy of Independent Systems which they continued to participate in until Mallie became pregnant. The son of Kento Marek and Mallie Marek, Galen was born with an extremely powerful connection to the Force. Galen Marek was a child during the early years of the Galactic Empire and the Great Jedi Purge. The son of Kento and Mallie Marek, both whom were Jedi, Galen Marek was born strong in the Force. "The dark side has clouded your mind, you killed my master years ago!" ―Darth Vader and Kento Marek " I sense someone far more powerful than you nearby.
As such, Vader kept his apprentice's existence a secret, bestowing to him the call sign "Starkiller." For years, Starkiller aspired to truly become one with the Order of the Sith Lords, believing it was his destiny to help Vader overthrow Sidious and usurp his throne as Galactic Emperor. Though trained in the Sith arts, the Rule of Two dictated that there could only be two Sith Lords at a time, and therefore Marek could not consider himself a true Sith while his master was still apprenticed to Darth Sidious. In time Marek forgot his past and even his birth name, having been taken from his home as a child by the Dark Lord. Gauging the orphan's raw strength in the Force, Vader abducted and ultimately raised Galen to embrace the dark side of the Force. As a target of the Great Jedi Purge, Kento was confronted and slain in a lightsaber duel by the Dark Lord of the Sith, who discovered the fugitive Jedi's son in the process. Following his mother's death, Kashyyyk was invaded by the Imperial Military. The son of two Jedi Knights, Kento and Mallie Marek, Galen was born on the Wookiee homeworld of Kashyyyk in the aftermath of the Clone Wars. Galen Marek (pronounced /ɡeɪlən ˈmæɹɛk/), codenamed Starkiller, was a Force-sensitive Human male taken on by the Sith Lord Darth Vader as his secret apprentice and personal assassin during the reign of the Galactic Empire. His sacrifice will only inspire them." ―Darth Sidious, on Galen Marek