The game is a first person shooter, based on the Republic Commando novels. In the game, the players play as Delta Squad, a team of Clone Commandos. The player can issue order's, convert their starting weapon and pick up enemy weapons.
Delta Squad is sent to the frontlines in the Battle of Geonosis, on a mission to execute Geonosian Leader named Sun Fac. After this is accomplished, they then sabotage the secret droid factory that was located beneath his base. Their next accomplishments were the destruction of an Anti-Aircraft Bunker and the stealing of Separatist Launch Codes, preventing the CIS ships from launching.
Delta squad has been sent to investigate the RAS Prosecutor, which went missing on a patrol, and upon returning, ignored all republic contact. Upon boarding the ship, they are attacked by Scavenger Droids who were sabotaging the communications onboard. In further areas, they find alien mercenaries and slavers, and kill them, and destroys their dropship. With a Trade Federation Ship on its way, they fend off waves of battle droids until reinforcements arrive, and then activate the ships defences to destroy the hostile battleship.
Delta answers a plea from the Wookies of Kashyyyk, and rescue General Tarrful from the Slavers and Mercenaries. After encountering CIS General Grievous and his Elite Guard, they discover an alliance with the Trandoshans and the Separatists. They then destroy a supply depot and begin a key and critical battle in Kachirho. After fending off Advanced Battle Droids, they destroy the large Kachirho Bridge and secure the Citadel. After fending off many Elite and Heavy forces, they are given the order to rendezvous to leave the planet. One commando, Sev, does not make it, and is left to die as Orders are given not to rescue him.