Stass Allie was stationed on Coruscant at the end of the war when the Separatist launched their desperate attempt to invade the Republic capital. Part of the Separatists' goal was to kidnap Chancellor Palpatine during the fighting. Confederate commander, General Grievous, infiltrated Palpatine's quarters in an attempt to kidnap the Chancellor himself. Stass Allie joined Shaak Ti, Foul Moudama, and Roron Corobb in shielding Palpatine from Grievous' attack. However, during the chase across Coruscant's cityscape, the cyborg general succeeded in capturing Palpatine and returning to orbit with him. Palpatine would eventually be rescued by Obi-Wan Kenobi and Anakin Skywalker who would also kill Count Dooku in the process. While General Grievous escaped, the death of Count Dooku signaled the beginning of the end of the Clone Wars.

After the Battle of Coruscant, Stass Allie was sent to Saleucami in the Outer Rim to clean up the resistance that remained following the siege led by Quinlan Vos and Aayla Secura. Sadly, while Stass Allie was patrolling the battlefields of Saleucami, Darth Sidious issued Order 66 and Allie's clonetroopers turned against her. Stass Allie was aboard a speeder bike when clone commander Neyo and his partner dropped behind Stass Allie and opened fire. Stass Allie was killed in the resulting crash and subsequent explosion becoming one with the Force and joining the scores of Jedi killed by clonetroopers that day.