The game begins with a montage detailing Delta Squad's creation, early life, and training at the cloning facilities on Kamino. At the onset of the Clone Wars, the four members of the squad—Delta-38, 62, 40, and 07 ("Boss", "Scorch", "Fixer" and "Sev", respectively)—are deployed during the Battle of Geonosis and tasked with assassinating Sun Fac, the chief lieutenant of Geonosian Archduke and Separatist Council member Poggle the Lesser. Upon successfully terminating their target, Delta Squad is retasked to several other objectives that were originally assigned to other Clone Commando teams that had been lost to enemy ambushes. The squad proceeds to sabotage a battle droid factory located underneath Sun Fac's headquarters, disable a major anti-aircraft bunker that is wreaking havoc on the Republic Army's air forces, and finally sneak onto a disabled Separatist Trade Federation Lucrehulk-class Core Ship both to sabotage the ship and to steal important launch codes that will be used to prevent a significant portion of the Separatist fleet from retreating. The squad narrowly escapes the Core Ship moments before it is destroyed.
