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. A year into the war, the now-veteran Delta Squad is sent to investigate the derelict
Acclamator-class Republic Assault Ship (RAS)
Prosecutor. Delta Squad splits up to investigate, quickly losing contact with command as they board the ship due to unexplained communication jamming. Making their way inside, they 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 logs from its data cores for investigation. As Boss is about to reunite with Sev, the latter is suddenly attacked and captured by a
Trandoshan who is part of a large force of slavers and mercenaries who have 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 who were held in the Assault Ship's brig, 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 a sizable force of battle droids. Delta Squad fights its way through the Trandoshan forces until they reach the hangars, where they destroy the Trandoshan dropship. Just then, a
Lucrehulk-class
Trade Federation Battleship drops out of hyperspace, arriving to complete the deal with the now-dead Trandoshans. As Republic reinforcements are still en route, Delta Squad defends the vessel against hordes of battle droids that are sent to board the Republic ship through its hangars. After successfully repelling the incoming droid forces and closing off the hangars, the Separatist Battleship realizes that Republic forces have regained control of the
Prosecutor, and so it begins opening fire on the ship. Delta Squad fight their way through droid boarders to reach the gunnery deck and activate the ship's turbolaser batteries to defend themselves. The timely arrival of a second Republic ship, the RAS
Arrestor, buys the squad enough time to activate the turbolasers. The combined fire of the two Republic Assault Ships ultimately destroys the Separatist Battleship which also shuts down all remaining battle droids on board. As the war drags on, Delta Squad continues to undertake dangerous missions. When the
Wookiee Chieftain
Tarfful, an important ally of the Republic, is captured by Trandoshan slavers on
Kashyyyk, Delta Squad is sent to find and rescue him. While making their way through the Trandoshan slave camp, they witness
General Grievous arriving in his personal ship, the
Soulless One, and are ordered to capture him if possible. The squad manage to rescue Tarfful but are too late to capture Grievous, and are left to fight his
MagnaGuards. Afterwards, deducing that the Separatists and the Trandoshans are working together, Delta Squad sabotages a Trandoshan supply depot, which was actually a staging area for the Separatists’ invasion of Kashyyyk . After destroying the depot, the squad is deployed to the city of Kachirho, setting in motion the
Battle of Kashyyyk. There, they move through the Wookiee tree city, securing important objectives and battling against hordes of advanced battle droids. Soldiering through Separatists forces, Delta Squad once again splits up to man four heavy anti-aircraft turrets to assist in the destruction of a Separatist destroyer hovering over Kachirho. Once the ship is destroyed, Clone Advisor CC-01/425 orders Delta Squad to regroup at Boss' position. However, Sev reports that he is under heavy attack before all communication with him is lost. Boss, Scorch, and Fixer prepare to rescue Sev, but are forced to abandon him when the Advisor orders them to evacuate immediately. As they head out on the gunship, they are debriefed by Jedi Master
Yoda. A huge Republic fleet is seen deploying outside the gunship, as the now three-man Delta Squad prepares for another assignment in the battle. ==Soundtrack==