At the outbreak of the Clone Wars, T'chooka had taken on a young Human named Flynn Kybo as his apprentice. The pair took on a myriad of missions during the course of the war that took them all across the galaxy. One such mission took T'chooka, Flynn, and a contingent of Jedi and clonetroopers to the planet of Vandos to extract the Anx ambassador Quiyyen. The Jedi had hoped to beat the Separatists to the planet before they invaded. Unfortunately T'chooka and Flynn found a large contingent of battle droids awaiting them, having arrived too late.

It would turn out that the mission to rescue the ambassador was a trap set in order to ambush the Republic forces. Nonetheless, the T'chooka and the Jedi fought the Separatist forces with hope of completing their mission. During the battle, the Separatist leader, General Grievous, personally dispatched a number of clonetroopers and even Jedi Knights. As the Jedi made their way out to the landing pad for escape, the Republic forces were dwindling and were becoming increasingly outnumbered.

It was then that T'chooka D'oon took the success of the mission into his own hands. Placing himself between the advancing General Grievous and battle droids, the Jedi Master hoped to slow them down long enough for Flynn, the ambassador, and the remaining troopers enough time to leave. As T'chooka engaged General Grievous, the alien cyborg brandished double lightsabers. Unfortunately, the Separatist general would have been more than a match for the Jedi Master had he wielded only one lightsaber.

On the landing platform high above the ravines of Vandos, General Grievous would prove victorious. With lightning fast speed, Grievous cleaved T'chooka D'oon into three pieces. Grievous finally achieved revenge against the man who, in his view, was the cause of much suffering of the Kaleesh people. However, T'chooka sacrificed himself to the Force in order to give his compatriots a chance to escape; T'chooka D'oon died a true Jedi Knight.