Following a montage that briefly details Delta Squad's creation, early life, and training at the cloning facilities on Kamino, the game begins with the team being deployed into the front lines of the Battle of Geonosis at the onset of the Clone Wars. There, team leader Delta-38 ("Boss", the player character) meets up with squad mates 62, 40, and 07 ("Scorch", "Fixer" and "Sev" respectively) as they are given their first assignment: to assassinate Sun Fac, chief lieutenant of Geonosian Archduke Poggle the Lesser, one of the members of the Separatist Council. Upon successful completion of their objective, Delta Squad sabotage the droid factory underneath Sun Fac's headquarters, disable an anti-aircraft bunker that is wreaking havoc on the Republic Army's air forces, and sneak onto a disabled Separatist Trade Federation Lucrehulk-class Core Ship to steal important launch codes to prevent the Separatist fleet from retreating; escaping moments before the ship is destroyed.
A year into the war, the now-veteran Delta Squad is sent to investigate the derelict Acclamator-class Republic Assault Ship (RAS) Prosecutor, their former home before being deployed to active duty. Delta Squad splits up to investigate, quickly losing contact with command as they board the ship. Making their way inside, the squad find the Prosecutor seemingly abandoned and in disrepair. The squad lose contact with Scorch after he reports electrical interference with his visor and Boss is soon ambushed by scavenger droids. Boss makes his way to one of the ship's data cores to reunite with Sev, but he is suddenly attacked and captured by a Trandoshan who is part of a large crew of slavers and mercenaries who’ve taken over the ship. Having evaded capture, Boss and Fixer meet up but are soon attacked by battle droids deployed by the Trandoshans. After rescuing their captive squad members, Delta Squad takes back the ship’s bridge and destroy a jamming device which reestablishes communication with command. It becomes clear that the Trandoshans intend to sell the vessel to the Separatists in exchange for battle droid dispensers. Making their way down to the hangars, Delta Squad then destroys the Trandoshan dropship during their retreat. Immediately afterwards, a Lucrehulk-class Trade Federation Battleship drops out of hyperspace. As Republic reinforcements are en route, Delta Squad defends the vessel against hordes of battle droids. After successfully repelling the incoming droid forces, the enemy Battleship begins opening fire on the Prosecutor. Delta Squad fight their way to the gunnery deck to activate the ship's turbo lasers in order to defend themselves. The timely arrival of a second Republic ship, the RAS Arrestor, buys the squad enough time to activate the turbo lasers, ultimately destroying the Separatist Battleship and shutting down all remaining battle droids on board.