The Evacuation of Rhen Var is a crushing defeat for the Republic, despite the planet's unimportance to Republic forces.
Geonosis is won, but the war has only begun. However, Windu is forced to lead a group of elite Republic commandos on a mission to take out any launching Separatist ships followed by defeating three Dark Acolytes. Once the transports reach the Petranaki arena, they unload their Jedi and rescue the heroes. With the planet defenseless, the duo is set off to eradicate the enemy forces at a nearby landing zone to clear way for the Republic transports carrying the Jedi. On Geonosis, Mace Windu and Luminara Unduli are sent to eliminate the planet's defenses consisting of a network of anti-orbital cannons prior to the arena battle. The bonuses are used to unlock features such as a 3D gallery of vehicles from the game, concept art, and an interview with the development team. Each mission consists of two to three objectives along with two to three bonus objectives.
There are 16 missions, grouped into six planets. The Clone Wars mostly consists of vehicular combat, although there are a few on-foot segments with Skywalker and Windu.
In the game, players switch between the Jedi characters of Obi-Wan Kenobi, Anakin Skywalker and Mace Windu of the Jedi Order.