Tsui Choi and the Jedi arrived as the Yinchorri were attacking the third strike team and jumped right into battle. Scores of Yinchorri soldiers backed by heavy weaponry and battle tanks charged at the twelve Jedi. The battle would result in the death's of three Jedi, including Tsui Choi's Padawan, Theen Fida. However, the Yinchorri command was not located on YInchorr either, leaving the Jedi nowhere to turn. Luckily, Jedi Master Yaddle discovered the existence of a fourth planet in the YInchorri system, Uhanayih, and the surviving Jedi traveled there backed by four Republic Navy attack groups sent by Chancellor Finis Valorum.

On Uhanayih, Jedi Master Saesee Tiin plunged the Republic cruiser directly into the heart of the Yinchorri command center where Tsui Choi and the Jedi emerged to demand their surrender. Master Choi and the Jedi then returned to Coruscant with their fallen Knights to honor them in death. Following the Yinchorri uprising, Tsui Choi did not take another Padawan and did not see battle again until decades later when the Clone Wars spread throughout the galaxy. Two months after the Clone Wars began, the Separatists launched an attack on Kamino in an attempt to deprive the Republic of its clone army.

The battle was under the command of Jedi Master Oppo Rancisis. Tsui Choi commanded Red Squadron alongside Aayla Secura, which was responsible for defending the Kaminoan cities from the Separatists' droid starfighters. Despite heavy losses, the Jedi and Republic forces were able to repel the attack and preserve the source of the army they would need to fight the war against the Separatists. During the course of the war, Tsui Choi found himself aboard a Republic troopship carrying reinforcements to Drongar when it was intercepted by a Separatist force. He fought alongside Jedi Knights Kai Justiss and Sian Jeisel, but the Separatists were able to board the ship and Tsui Choi found himself face to face with the leader of the Confederacy of Independent Systems and former Jedi, Count Dooku.

Dooku was joined by traitor to the Jedi Order, Sora Bulq, who had been corrupted by the Sith Lord and had fallen to the Dark Side. Tsui Choi and the Jedi felt they would certainly be put to death by Dooku, but in an effort to draw more Jedi to their side by showing mercy, Count Dooku arranged a shuttle to take the Tsui Choi and the Jedi to neutral territory. At the end of the war when Palpatine issued Order 66, Tsui Choi managed to survive and went into hiding. Alone and on the run for a month, Tsui Choi eventually ended up on Eriadu where he made contact with fellow survivor Bultar Swan.