Years later, after the outbreak of the Clone Wars, Quarmall found himself in the care of the Bergruutfa clan made up of six, young Padawans which included Allara, Banz, and the Whipid Padawan Tak-Tak. Due to the declining numbers of the Jedi in the preceding decade as a result of the Separatist crisis, they Jedi often found themselves short on manpower. Recognizing this potentially crippling problem, Quarmall took it upon himself to accept all six members of the Bergruutfa clan as his apprentice. It was a move that was very controversial among the Jedi, but as they could not disagree with his reasoning, simply chose to look the other way.

While traveling on a Mon Calamari star cruiser with his Padawans, Quarmall and the Mon Calamari found themselves under attack by Grievous and his forces. Boarding the ship unleashed dozens of battle droids to cut down the Mon Calamari soldiers. Knowing what Grievous would do if he found the Padawans, Quarmall hid them in a storage compartment during the battle. While the battle raged, the Abyssin Jedi came face to face with Grievous in the corridors of the ship. Surrounded and outnumbered by battle droids, there was little Quarmall could do when Grievous ordered them to open fire. Cut down in a hail of blaster fire, Jedi Master Quarmall became one with the Force. While Grievous did locate and kidnap Quarmall's Padawans, they were eventually rescued by a team of Jedi made up of Flynn Kybo, Jedi Master B'Dard Tone, and his Padawan, Codi Ty.