

Rex created an algorithm to fight the Separatists, which the Separatists had discovered. Jedi General Anakin Skywalker and High General Mace Windu lead the 501st Legion and 91st Reconnaissance Corps to Anaxes to reclaim the planet under Admiral Trench‘s forces. Fives would go on to investigate the chips, resulting in his death at the hands of Commander Fox. Tup would die when his inhibitor chip got removed by Fives. Tup and Fives went to Kamino to discover what happened to him. The battle lead to Tup executing Tiplar after the control chip malfunctioned, causing him to execute Order 66 pre-maturely. Jedi General Anakin Skywalker, Jedi General Tiplar and Tiplee lead the 501st and Doom's unit lead by Captain Rex and Commander Doom. It was later revealed that Krell was a traitor and was executed by clone trooper Dogma. Many of the 501st's troopers expressed their disdain for their General, resulting in a split in the ranks.

The Legion sustained heavy casualties due to Krell's poor leadership to gain victory. General Krell later took charge of the mission in replace of General Skywalker. The Republic sent the 501st Legion lead by Jedi General Anakin Skywalker and Captain Rex and the 212th Attack Battalion lead by Jedi General Obi-Wan Kenobi and Commander Cody to retake the planet with an invasion. Later in the war, the planet Umbara withdrew from the Republic and joined the CIS.

The 501st held their own during the battle, with two troopers, Echo and Fives, getting promoted to ARC troopers due to their amazing performance. Battle of KaminoĪfter General Skywalker and Kenobi intercept a transmission of Ventress and Grievous planning an attack on Kamino they then sent the 501st Legion to Kamino to defend the planet. Later Obi-Wan Kenobi arrived with 212th Attack Battalion to back up Torrent Company and they won. Few of Torrent Company survived including Rex. However, they were able to win in the first wave but in the second wave, they were forced to retreat. The 501st commanded by Anakin Skywalker and his padawan was dispatched to Teth in order to recover Hutt crime lord Jabba the Hutt's son, Rotta, in order to gain access to hyperlanes passing through Jabba's territory for the Galactic Republic. Jedi Generals Anakin Skywalker and Obi-Wan Kenobi lead the 501st Legion along with the 212th Attack Battalion under the commands of Captain Rex and Commander Cody to liberate the planet from the Separatists invasion.

Rex and his troops fight on Christophsis. Later in the final days of the Clone Wars, Anakin Skywalker now known as Darth Vader lead the 501st under Commander Appo to attack the Jedi Temple. The 501st Legion was temporarily put in-charge of General Krell who secretly was an agent of Dooku. The 501st clone battalion fought in many battles during the Clone Wars, under Jedi General Anakin Skywalker and Captain Rex. 3.16 Unidentified Galactic Republic Division.
