Anakin and Ahsoka are on Ryloth and have to clear the way for the Clone troopers by fighting through various amounts of droids.
Meanwhile, the Juma 9 station is under attack so Obi-Wan, Plo Koon, Commander Cody and Switch must stop it. While going to the comms room, Obi-Wan and Plo find a Skakoan scientist there. They follow him, and he reveals himself to be Kul Teska. After a battle, he escapes but Obi-Wan and Plo get trapped.
Since Anakin has lost contact with Obi-Wan and Plo Koon, Jedi Masters Mace Windu and Kit Fisto (as well as Commander Ponds), arrive to rescue the trapped pair.
On Alzoc III, Aayla Secura, Luminara Unduli, Commander Bly and Commander Gree try to solve the puzzle of floating debris of a CIS ship. They discover it was destroyed by a mysterious weapon and alert the others right away. Eventually the two end up facing Dark Jedi Asajj Ventress which was dispatched by Dooku to get rid of any witnesses.
Back on Ryloth, Captain Rex and Boomer are captured by Cad Bane and told to load a Separatist Superweapon (which caused the floating debris on Alzoc III) aboard his ship, but the droids want it back. So the two clones have to stop them. Anakin and Ahsoka then come in to save the two clones but then they also have to stop the droids, too. Eventually, the five get out of the cave and Rex and Boomer decide to destroy all of the droids, leaving time for Anakin, Ahsoka, and Bane to get to his ship. When they arrive in the junkyard, they find Kul Teska.
Teska escapes so Ahsoka and Anakin contact Obi-Wan and Plo Koon only to find that Aayla, Luminara and Yoda contacted them as well. They all find out that Padmé Amidala has been captured by Teska, on Behpour, who has been planning with Dooku to destroy the Naboo Star System with the superweapon. Anakin, Obi-Wan, Ahsoka, and Mace Windu go to destroy the superweapon. In the assault, Anakin and Obi-Wan sneaked into the facility to deactivate the Deflector shield generator, while Ahsoka and Mace Windu led the charge into the facility. After a fierce assault, Obi-Wan and Windu found Count Dooku and eventually defeat him. Anakin and Ahsoka, on the other hand, fought Teska and barely escaped the facility with the rescued Senator Amidala on two Single Trooper Aerial Platforms.
In the first mission, Obi-Wan, Cody, Anakin, Ahsoka and some Clone troopers traveled to Christophsis to take out a ray shield and protect their heavy cannons.
While Kit Fisto traveled to Grievous' lair to find Nute Gunray. Ahsoka, Obi-Wan and Mace Windu go to Ryloth to save the inhabitants from the Separatists.
Cad Bane had been captured by a Droid base, and he had valuable information to the Republic, so Kit Fisto and Padmé Amidala traveled there to get that information.
R2-D2 had been captured by Grievous for the Republic tactics and base locations hidden within him. On Skytop Station, Ahsoka, Anakin and Rex started a desperate hunt for R2. When they found him, they had to race against time to get off the falling ship. Meanwhile, Luminara Unduli and Gree returned to Grievous' lair to get codes that were revealed to be hidden there by Cad Bane's information.
This is based on the movie and episodes from Seasons 1 and 2.
The game allows players to play as Jedi Knights, clone troopers and other characters, and contains 40 missions. The gameplay changes on certain missions. On missions with Jedi characters, it is platforming based. On missions with clone characters, it is third-person shooter-based.
Join The Clone Wars promotional wallpaper featuring Captain Rex.
Republic Heroes was promoted online through an interactive website and advertisement campaign known as Join The Clone Wars, hosted at LucasArts. It contains three main components: HoloNet News, Train, and Holocomm. The HoloNet News section contains six news items and video clips that were progressively released in the build-up to the release of the game. These clips are accompanied by in-universe text blurbs in the form of news bulletins. The Train section contains two mini-games, Jedi Force Jump and Clone Weapons Training. These mini-games mirror the setting of the video game itself, and they also allow up to thirty players to join together in a platoon. The Holocomm section has a video briefing designed to link with a webcam. When entering the promotion, users generate a character by specifying a homeworld, droid companion, starship, race and other variables. From this, the site generates several character names.
The Nintendo DS version includes a databank which features information on various aspects of The Clone Wars series, which do not appear and are not mentioned in the actual game.