Set in between the events of the series' first and second season, the game follows the adventures of multiple characters during the Clone Wars, which eventually come together by the end of the game. The story begins with the Battle of Ryloth, where Anakin Skywalker and Ahsoka Tano are leading an assault on a Separatist stronghold, having to clear the path of battle droids to allow their clone troopers to advance. Meanwhile, the Separatists attack the Republic's Juma 9 space station, where Jedi Masters Obi-Wan Kenobi and Plo Koon, Commander Cody and clone trooper Switch try to fend them off. On their way to the comms room, Obi-Wan and Plo find a heavily-armored Skakoan scientist and follow him. Cornered, he reveals his name to be Kul Teska and battles the two Jedi before making his escape, leaving Obi-Wan and Plo trapped. Having lost contact with Anakin and Ahsoka, they instead call Mace Windu and Kit Fisto, who, along with Commander Ponds, rescue them.
On Alzoc III, Jedi Masters Aayla Secura and Luminara Unduli, and Commanders Bly and Gree lead an investigation on supposed Separatist sightings, reported to them by Jabba the Hutt. They come across floating debris leading to a crashed Separatist ship, which they discover was destroyed by a superweapon the Separatists are developing. After informing the Republic, they are attacked by Asajj Ventress, who was dispatched by Count Dooku to kill any witnesses. Aayla and Luminara duel Ventress and manage to trap her inside an ice cave.
Back on Ryloth, Captain Rex and Sergeant Boomer are captured by the bounty hunter Cad Bane, who orders them to load a key component of the Gravitic Polarization Beam (the Separtist superweapon which caused the floating debris on Alzoc III) aboard his ship. When they are attacked by the Separatists' battle droids, Bane reluctantly releases the two clones to help fend them off. Shortly after, Anakin and Ahsoka arrive and help eliminate the remaining droids, before agreeing to help Bane load the superweapon into his ship, not wanting it to fall into the Separatists' hands. While Rex and Boomer stay behind to fight droid reinforcements, Anakin, Ahsoka, and Bane deliver the Gravitic Polarization Beam to the latter's ship, where they are attacked by Kul Teska, who came to claim back the superweapon after Bane stole it from him on Alzoc III. As Bane makes his escape, Anakin and Ahsoka attempt to fight Teska, but he manages to flee with the superweapon.
Anakin and Ahsoka contact Obi-Wan, Plo Koon, Mace Windu, Kit Fisto to discuss the situation; they are soon joined by Yoda, Aayla Secura, and Luminara Unduli. After learning that Teska and Dooku plan to use the Gravitic Polarization Beam to destroy the sun of the Naboo Star System, and that the Separatists captured Senator Padmé Amidala after she stumbled upon their secret base on Behpour, the group plans a full-scale invasion of the planet to retrieve or destroy the superweapon, and rescue Padmé. Commander Cody and Captain Rex create a distraction that gives Anakin and Obi-Wan enough time to infiltrate the Separatists' base and destroy its deflector shield generator, allowing the main body of clone troopers, commanded by Windu and Ahsoka, to storm the base.
Inside the base, Anakin and Ahsoka make their way to Teska's lab to confront him, while Rex, Cody and Ponds clear the path of battle droids for the Twilight ship to land at the rendezvous point. While waiting for the others to arrive, however, Count Dooku attacks and traps them inside the ship using the Force, which he then throws off the platform it was standing. Moments later, Obi-Wan and Windu arrive to duel Dooku, but during their fight the platform collapses; Dooku is picked up by Ventress in her ship and the pair escape, while the Jedi are rescued by R2-D2 flying the Twilight. Meanwhile, Anakin and Ahsoka defeat Teska (with some unexpected help from Cad Bane), before rescuing Padmé, who has sabotaged the Gravitic Polarization Beam. The trio manage to escape from the base moments before the superweapon explodes, killing Teska and destroying the base. They rendezvous with the others outside, whereupon the Republic celebrates its victory. In a post-credits scene, it is revealed that Bane sabotaged Dooku and Ventress' escape ship.