Whorm being distracted by this, was taken hostage by General Kenobi, ending the battle as a Republic victory.After the Battle of Christophsis, Cody and the 212th Battalion accompanied General Kenobi during his meeting with Jabba the Hutt on Tatooine.Cody later helped the other clones along with cadets to set up an ambush for Grievous and his droids that were clearing out the barracks, while Kenobi engaged Grievous in a short duel.While the clones were battling the incoming droids, 99 tried to run back to the armory to resupply the clones whom Cody ordered him to stop, but due to his slowness was ultimately shot in the back.
Some time after this, Cody was joined on the front lines by Skywalker to defeat the first wave of droids commanded by General Whorm Loathsom but eventually was forced to retreat when the Separatist tanks overwhelmed the republic artillery.
With the support and recommendations of General Kenobi he rose to Marshal Commander, the highest rank a clone can hold.
During the campaign, they were able to root out a traitor amongst themselves; a sergeant by the name of Slick, who had divulged intelligence to Count Dooku's apprentice Asajj Ventress for credits.
He and his men were tasked to assist the 501st Legion, General Skywalker and his apprentice Ahsoka Tano during their mission to rescue Jabba's son Rotta, who had been kidnapped and brought to a Separatist controlled prison on Teth.
When Cody and Rex were dispatched to inspect the Rishi moon station, they were welcomed by what appeared to be a clone trooper, but in fact was a commando droid appropriating his armor.