Eventually, the Yinchorri uprising came to an end and things around the Jedi Temple returned to relative normality. Over the next twenty years, Soon Bayts grew into a fine Jedi Knight, attaining the rank of Jedi Master even. When the Clone Wars broke out, the signs of age began to show around Soon Bayts' temples in the form of some graying hair. A few years into the war, Soon Bayts found himself part of a mission to investigate a blockade around the backwater planet of Boz Pity. The mission was headed up by many, many great Jedi Masters including Adi Gallia, A` Sharad Hett, Saesee Tiin, Kit Fisto, Plo Koon, Ki-Adi-Mundi, Agen Kolar, Mace Windu, Obi-Wan Kenobi, and Jedi Knight Anakin Skywalker.

The Jedi would be taking only a single capital ship, so they needed to come up with a plan to get past the blockade and onto the planet. Hinging the success of the mission and the lives of everyone on board on Anakin Skywaker's famous piloting skills, Soon Bayts and the Jedi developed a plan to make the reversion from hyperspace between the blockade and the planet, a maneuver that would require nanosecond timing. The plan almost work, or worked well enough. While Master Bayts and the Jedi found themselves behind the blockade's lines, they were too close to the planet's gravity well to escape its pull. They would be going in on a crash landing.

With Jedi Master Saesee Tiin commanding the orbital forces, the Jedi Master managed to get his squadrons deployed before the ship entered Boz Pity's atmosphere. Soon Bayts and the rest of the Jedi made up the ground forces that would seek to take the enemy's base. While many of the Jedi Masters believed the Dark Jedi, Asajj Ventress, to be dead, Master Kenobi had been following a trail of clues that led him to believe that she was alive and hiding on Boz Pity. He warned Soon Bayts and the rest of the Jedi to be prepared for the possibility that they might have to face her.

Unfortunately for Master Bayts, the clues Obi-Wan had followed were valid; they simply led to the wrong person. As the Jedi launched their attack against the Separatist base, General Grievous emerged to confront them. Grievous had been the one to leave the clues Obi-Wan had been following, and while not a Dark Jedi like Ventress, the cyborg general was perhaps a more dangerous foe. Fighting alongside Adi Gallia, the pair were not prepared for the ferocity with which Grievous came at them. With one of his four arms, Grievous grasped Soon Bayts' skull and crushed it with no effort whatsoever. Jedi Master Bayts became one with the Force that day on Boz Pity, another casualty of the Clone Wars and the Jedi Purge.