During the Battle of Kashyyyk, Supreme Chancellor Palpatine—secretly Darth Sidious—transformed the Republic into the Galactic Empire, the Jedi Order was destroyed through Order 66, and the Clone Wars came to an end. In the aftermath of the "Jedi insurrection," the false story which legitimized Order 66 and the Great Jedi Purge for the Republic, Commander Faie and the clones became loyal to the new Empire and began to hunt down Vos. During the search, the troops prepared to lay waste to a Wookiee village, which caused Vos to intervene. Though wounded, he struck down Faie and later escaped Order 66 and the Empire along with his new lover, Khaleen Hentz. Meanwhile, Vos was presumed dead by the Coruscant Security Force. Vos was supposedly implicated in the insurrection, though CSF Inspector Divo kept silent on the matter of whether Vos was dead or alive. Some time after Order 66, Vos was listed among priority targets for the Inquisitors of the presumed survivors of the new Galactic Emperor's Jedi purge.[35] During the invasion of Mon Cala, Jedi Padawan Ferren Barr and Verla, his informal apprentice, escaped an engagement with a trio of Inquisitors. As they parted ways following their escape, Barr told Verla to find another surviving Jedi to help train her, listing Vos among the possible survivors she could turn to, having found no death records for him.
