Sometime during the thousands of years between the fall of the Eternal Empire and the Galactic Civil War, an incarnation of HK-47 was recovered and was aboard a Hammerhead-class cruiser which crashed on the volcanic Outer Rim planet of Mustafar. Thousands of years later, a tectonic shift exposed the cruiser. When the Confederacy of Independent Systems arrived on Mustafar during the ongoing Clone Wars, they discovered the wreckage and the deactivated HK-47, which was still in excellent condition. When Separatist engineers managed to turn the droid back on, it went on a rampage. It killed several of the engineers and destroyed three B2 super battle droids and even a droideka with ease, before the remaining engineers could power him down via a restraining bolt installed before his reactivation. The Separatist experts were amazed by the technology used in this droid, but were unable to perform a memory wipe due to its incomprehensible thought matrix.
A year and a half later, after the Battle of Christophsis, a squadron of Y-Wings, led by Moff Tycho Celchu, found the wreckage of the cruiser, and it was declared a war prize. Celchu tried to make the droid operational, but was unable to do so. 827ec27edc