When the Separatists launched an invasion of Kamino, Cody and Rex all but insisted that they join the mission to push the invaders back. Kamino was their home, and as Cody noted, that made the attack personal for the clones.

Cody assisted Obi-Wan during the mission to rescue Even Piell and Captain Tarkin from the feared Separatist prison known as the Citadel, fighting both battle droids and the facility’s numerous traps and defenses.

Warden Osi Sobeck’s droids captured Cody, Obi-Wan and Even Piell – but R2-D2 and his team of reprogrammed pilot droids intercepted their captors on the way to the interrogation room, taking over the guard detail and leading the “prisoners” to the shuttle. The getaway plan failed when more Separatist forces arrived, forcing the Jedi and clones to flee once again.

The Republic launched a rescue mission, but the Jedi and clones had to reach the extraction point, which required a perilous journey through the caverns of the planet Lola Sayu. Cody, Rex, Fives and the other clone troopers had to fight off droids and anoobas to survive.

Cody’s 212th Legion faced a particularly difficult test on Umbara: the Separatist-allied Umbarans had advanced weaponry; gloomy conditions and hostile fauna made fighting difficult, and General Pong Krell betrayed the Republic. Krell manipulated the 212th Attack Battalion and 501st Legion into battling each other, resulting in the death of veteran clones by friendly fire.

After the peaceful planet of Kiros fell silent, a team of Jedi and clones discovered the planet’s people had been carried off by Zygerrian slavers. Cody brought a disturbing message from the Separatist commander – if Obi-Wan didn’t surrender, Separatist bombs planted throughout the city would detonate.

After Hondo Ohnaka’s pirates captured Ahsoka Tano, Obi-Wan and Cody rushed to the aid of the Jedi younglings Ahsoka had been escorting. But General Grievous had other plans. He attacked Obi-Wan’s task force, requiring the Jedi General and Cody to engineer a quick getaway. The younglings’ rescue would have to wait.

In the final days of the war, the Republic received word that General Grievous was hiding on Utapau. Cody and his forces waited in orbit while Obi-Wan investigated the situation, verifying that Grievous was there. The Jedi gave the signal for Cody to join the fight, then confronted Grievous as Cody led his soldiers into battle against a variety of Separatist droids.

During the Battle of Utapau, Cody received Order 66, the directive to kill the Jedi, via an encrypted transmission from Darth Sidious. Obeying his clone indoctrination, Cody ordered his troops to open fire on his longtime Jedi General and friend.