While battling Separatists on Christophsis, Commander Cody and Captain Rex learned there was a mole within the Republic base. Both clones were shocked to discover the traitor was one of their own.

An unrepentant Sergeant Slick claimed the Jedi had enslaved the clones, and he wanted his clone brothers to be more than their pawns. Cody listened impassively, unwavering in his loyalty to the Republic he’d been born to serve.

During the battle at the Teth Monastery, Cody coordinated the gunships and troops as they landed to backup Obi-Wan Kenobi and the troopers of Torrent Company. Cody and his troops quickly turned the tide of the battle, which up until that point had not been going well for the Republic.

Cody and Rex discovered that droids had taken over the communications base on the Rishi moon, leaving only three surviving rookie clones. After leading the young clones in a successful attack to retake control of the station, Cody, Rex, and the rookies alerted the Republic fleet in time to fend off General Grievous' planned attack on Kamino.

After landing with Obi-Wan Kenobi and Ghost Company on the planet Ryloth, Cody and other scouts in the Company discovered that the Twi'leks were being held hostage.

Cody led his troops in a diversion to distract a portion of the droid army on Ryloth while Obi-Wan led forces to free the hostages. Ordering his men to fall back, Cody lured the droids away from the hostages.

During the Republic invasion of Geonosis, Cody found himself with a hard fight against tough odds, defending a Republic landing zone alongside Obi-Wan and exhausted clone troops. Cody and his men held out long enough for the Republic to gain a foothold on the planet.

After helping lead the troops to a successful landing on Point Rain, Cody accompanied Kenobi and Anakin Skywalker into the Progate Temple, where Luminara Unduli had been captured by Geonosian zombie drones. After Kenobi and Skywalker's attempts to negotiate with the Queen, who controlled the drones, failed, Cody and his troops buried her under rubble by bringing down the entire temple.

After General Grievous captured the Jedi Master Eeth Koth, Obi-Wan Kenobi, Anakin Skywalker and Adi Gallia launched a rescue effort in the Saleucami system. As a diversion, Obi-Wan lured Grievous onto his own ship while Anakin and Adi raced aboard Grievous’s craft to find Koth. Cody and his troops tried to capture Grievous as he rushed to return to his own ship, but the Separatist warlord managed to escape.

Grievous crash-landed on Saleucami in a damaged landing craft, and Obi-Wan and Cody pursued him down to the surface. Rex led one team in search of Grievous, while Cody and Obi-Wan led the other. Data from a battle droid led them to Grievous’s landing site, but the Separatist general made yet another getaway.

When Duchess Satine traveled from Mandalore to Coruscant, Cody was one of the leaders of the troopers assigned to protect her. But someone had smuggled assassin droids aboard the duchess’s luxury liner – and then the Separatists intercepted the vessel.

The Separatists attacked Satine’s luxury liner with Super Battle Droids. The elegant corridors of the Mandalorian ship were filled with blaster fire as Cody and his clones repelled the droid attack.

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.