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During the Yinchorri Uprising of 33 BBY, Soon Bayts was tasked with keeping track of the Jedi strike teams sent to the Yinchorri System. When the Jedi Temple on Coruscant was attacked, Bayts fought alongside the other Jedi to defend it from the Yinchorri threat. Following the battle, he received word from Masters Eeth Koth and Adi Gallia, determining that Yinchorri command was not located on Yitheeth as had been suspected. He also learned that Mace Windu's strike team had not engaged the opposition, and was lying in wait on Yinchorr. Delivering this news to Yoda, he encountered the Grand Master interrogating a Yinchorri survivor of the battle.

Bayts was curious as to how Yoda had made the prisoner so fearful, but the Grand Master explained that the warrior had brought the fear with him when he attacked the temple, and that he had simply shown him the reality of it. While Bayts delivered his message, the warrior made to attack Yoda, inciting the younger Jedi to leap to the Grand Master's aid. Yoda, however, simply levitated Bayts as he deflected the warrior's attack, and shoved the warrior into the wall, incapacitating him. Yoda then reprimanded Bayts, telling him that emotion had clouded his judgment.

Shortly thereafter, Bayts received further reports from the Yinchorri system: All three strike teams had rendezvoused on Yinchorr, and a Devaronian prisoner had been taken. Upon delivering the news to Yoda, Bayts speculated that the Devaronians might have been behind the mysterious uprising. Later, Master Windu called with urgent news about the Yinchorri command center's location, and Bayts once again had to rush into Yoda's presence, alerting him to the situation. The uprising was eventually quelled thanks to the efforts of the strike teams, though three Jedi perished in the conflict.

By the time of the Clone Wars, Soon Bayts had ascended to the rank of Jedi Master. For unknown reasons, he changed the color of his lightsaber blade from orange to blue. Along with Mace Windu and several of the Jedi, among them veterans of the Yinchorri Uprising, he accompanied Senator Bail Organa of Alderaan on the Venator-class Star Destroyer Intervention, bound for the Outer Rim Territories. Alderaan had many ties to the Outer Rim worlds, and when Organa learned that the Confederacy of Independant Systems was retreating there, he felt the need to witness the battles firsthand.

Based on intelligence from Master Obi-Wan Kenobi, the Intervention journeyed to Boz Pity, where a large Confederate blockade was known to be amassing. Since they were but one ship against an entire flotilla, the Jedi enlisted Anakin Skywalker, to help pilot the capital ship through the blockade, resulting in a crash landing on the planet's surface. Master Bayts ventured out with Adi Gallia, Senator Organa, and a detachment of clone troopers.

The group met heavy resistance at the Confederate base, fighting off hordes of battle droids. Organa called for a charge, and the two Jedi obliged. As Bayts and Gallia cut their way through to the opening of the base, they encountered the Kaleesh cyborg General Grievous. Before Bayts could even attack the general, Grievous grasped his head with one of his mechanical claws, and crushed it, killing the Jedi Master instantly. The General then took Bayts's lightsaber, and used it to attack Republic troops. Gallia perished shortly thereafter. The Battle of Boz Pity was eventually won by the Republic, however.

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