On Geonosis, Mace Windu and Luminara Unduli are sent to eliminate the planet's defenses consisting of a network of anti-orbital cannons prior to the arena battle. With the planet defenseless, the duo is set off to eradicate the enemy forces at a nearby landing zone to clear way for the Republic transports carrying the Jedi. Once the transports reach the Petranaki arena, they unload their Jedi and rescue the heroes. However, Windu is forced to lead a group of elite Republic commandos on a mission to take out any launching Separatist ships followed by defeating three Dark Acolytes. Geonosis is won, but the war has only begun.
The Evacuation of Rhen Var is a crushing defeat for the Republic, despite the planet's unimportance to Republic forces. The Republic forces on Rhen Var (which are too small to combat the invasion) are allowed to escape the planet with minimal casualties because of the organized teamwork of Jedi Obi-Wan Kenobi and Anakin Skywalker. Before the battle, the two Jedi detect an invasion force and rush to Rhen Var to evacuate forces.
However, as the final outpost prepares for evacuation, the Confederacy attacks, forcing Anakin to single-handedly fight to prevent the outpost from being destroyed. As the evacuation completes, the Confederacy begins to destroy the Outpost.
The battle of Raxus Prime.
One month after the Battle of Geonosis, and shortly after the Evacuation of Rhen Var, the Republic detects unusual activity on Raxus Prime, and sends a strike force led by Anakin and Obi-Wan to investigate the activity.
On arrival, Anakin and Obi-Wan begin to scout out the area on the planet's surface. After they take out an enemy scout party, they discover an enemy excavation site and contact their assault ship for reinforcements.
Anakin and Obi-Wan make an attack on three supply convoys to stall for time so their strike force can land. Once the strike force lands, they fight their way to the excavation site, hampered by traps and surprise attacks. Eventually, they reach the excavation site, where there is a second group of Republic forces lying in wait. They destroy the shield generator, allowing the second strike team to enter the battlefield. Both teams simultaneously attack and destroy the remaining defenders, as well as the excavation cranes' fuel lines.
As the battle winds down, Anakin spots Count Dooku escaping in a Hardcell-class interstellar transport and pursues him. Once the Techno Union ship lifts off, the Confederates unleash their deadly assault machine, the Protodeka. The Protodeka destroys the entire Republic strike force. Obi-Wan single-handedly destroys the war machine, but by the time reinforcements arrive, Dooku's ship has already left the system with Anakin and a large excavated component.
After his encounter with Count Dooku on Raxus Prime, Anakin is captured and sent to Alaris Prime, the Kashyyyk moon, to be executed. Anakin and the other prisoners, including the mercenary Bera Kazan, are doomed to be killed by the component Dooku excavated from Raxus Prime: the Force Harvester, an ancient Sith weapon that drains the Force from all living things within its range. Using the Force, Anakin is able to break free from his cell, along with Bera. After freeing the other prisoners they escape on stolen Single Trooper Aerial Platforms. Moments later, the Harvester becomes fully charged and begins absorbing power from the moon's forest. Anakin and Bera navigate through the terrain to escape from the Harvester's blast radius. Eventually, they pass through a small Wookiee village (it is up to the player, whether to alert them of the danger coming their way), and the Force Harvester's power starts to recede.
Anakin and Bera retreat to a hidden Wookiee village where they learn that the CIS has jammed all planetary communications. Together they devise a plan to contact the Republic. Using a stolen Armored Assault Tank, Anakin and Bera infiltrate a CIS communication outpost and send a distress signal to the Republic. Shortly afterwards, the CIS attack the single remaining Wookiee village on the moon. With the use of traps, Anakin and Bera are able to block enemy reinforcements coming in through the canyons. However, they are unable to set up traps north of the village where the bulk of the enemy's army is entering. They are forced to hold off the enemy until the Republic fleet arrives. During the battle, Republic forces (with Obi-Wan in charge of the attack) arrive and are able to chase off the CIS army. Anakin and Obi-Wan trace the army back to its source: a Separatist dropship called the Harbinger. Together they destroy the Harbinger, severing the endless flow of CIS war machines. Bera survives the battle but her fate is unknown. The forests were reduced to waste by the Force Harvester and the multiple battles, forcing the native Wookiees to leave and find a new home.
When Anakin and Obi-Wan return to their headquarters, they report the happenings on Alaris Prime to Yoda and Mace Windu. Windu reveals to Anakin and Obi-Wan that during the Great Sith War, the Sith constructed a weapon so powerful that no one could withstand it. It was called the Dark Reaper, and it required tremendous amounts of energy to function. The Force Harvester gathered the required energy for the Reaper, allowing it to work. Mace also reveals that one Jedi, Master Ulic Qel-Droma (who would later fall to the Dark Side but eventually return to the Light Side), learned how to withstand the Reaper's effects. He taught others how to do it also, and the Jedi were able to defeat the Dark Reaper. After the war, the Jedi scattered the remaining pieces of the Dark Reaper to the far corners of the Galaxy and Anakin quickly works out that Dooku has now found those pieces; Windu tells them that if Dooku successfully reactivates the Dark Reaper, then they won't stand a chance against it. He also says that, after the war, Qel-Droma sought refuge on Rhen Var, which is also where his tomb is located. Knowing that's the one place they need to go in order to learn how to defeat the Dark Reaper, Obi-Wan and Anakin prepare a strike force to retake Rhen Var.
Obi-Wan and Anakin launch a massive assault on Rhen Var with Anakin fighting in the air and Obi-Wan on the ground. The sheer force of the attack overwhelms the Confederates, and Obi-Wan is able to lead his forces to the temple. At the temple, Anakin is met with spectral guardians protecting Qel-Droma's tomb. He defeats them and Qel-Droma appears before him, telling him that he's passed the tests. He tells Anakin he can teach him how to defeat the Dark Reaper but warns him that the power comes with great risk of him falling to the dark side.
The Dark Reaper
Anakin returns and informs Windu and Yoda that the Dark Reaper is buried on Thule. Based on the information Anakin has given them, they prepare their attack. Anakin and his strike force take out the planetary shield on the Thule moon, Sivvi. This allows Obi-Wan to perform an aerial attack on significant strategic locations across Thule in a Low Altitude Assault Transport. He destroys the Command Installation to cripple the Separatists' communications. Windu then commands the ground forces around Thule's capital city of Kesiak. Upon his arrival, Cydon Prax destroys Windu's TX-130 Saber-class fighter tank. Windu is forced to travel on foot to open the gates to the Sith Temple. Finally, Anakin and his strike force enter the Sith Temple. Anakin then kills Cydon Prax, allowing him to press forward. Because Anakin is the only commander who is immune to the effects of the Dark Reaper, he then defeats it with Qel-Droma's guidance. However, the knowledge he gained from Qel-Droma causes him to act more arrogantly towards Obi-Wan. He takes another indirect step towards the path to the Dark Side of the Force. Meanwhile, Dooku is nowhere to be found and Windu remarks to Yoda that the victory on Thule will turn the tide of the war. Yoda replies "The battle we have won. But far from over, this war is".
In the game, players switch between the Jedi characters of Obi-Wan Kenobi, Anakin Skywalker and Mace Windu of the Jedi Order. The Clone Wars mostly consists of vehicular combat, although there are a few on-foot segments with Skywalker and Windu.
There are 16 missions, grouped into six planets. Each mission consists of two to three objectives along with two to three bonus objectives. The bonuses are used to unlock features such as a 3D gallery of vehicles from the game, concept art, and an interview with the development team.
The multiplayer element of the game has four different game types: Conquest, Control Zone, Academy and Duel. Each game type is divided among several locations such as Geonosis or Thule.
Conquest divides up to four players on to two teams: the CIS and the Republic. Each team attempts to control as many outposts as possible until they have enough strength to destroy the opposing team's home base. Each outpost is capable of constructing four turrets and two Armored Assault Tanks or All Terrain Experimental Transports (depending on the team). This version is played on Rhen Var, Geonosis, Thule Moon, and Kashyyyk. The Republic players can control either a TX-130 Saber-class fighter tank or an All Terrain Experimental Transport. Separatist players can control a Ground Armored Tank or an Armored Assault Tank.
In Control Zone, you must fight to be the only one in a certain zone for a certain amount of time or until a certain number of points has been reached. You get one point per second in the Control Zone and one for killing a player.
In Duel, two to four players battle each other until a certain number of points or a certain time limit is reached. The player with the most number of points by the time limit or the first player to reach the score limit wins.
Playable vehicles in Duel and Control Zone include TX-130 Saber-class fighter tanks, All Terrain Experimental Transports, Armored Assault Tanks, Hailfire Droids, and Ground Armored Tanks.
The Academy training game is all about survival. One to four players try to survive as many waves of enemies as possible. Each wave, the number of enemies and their type changes. Every third round is either a duel or a bonus round (in the Thule Moon version). There are only two locations for this game type, and they are both different. In the Geonosis version you try to survive waves of Battle Droids, Super Battle Droids, Dwarf Spider Droids and Geonosian warriors while playing as a Jedi Knight or another character. The Thule Academy version has you locked in an All Terrain Experimental Transport or a TX-130 Saber-class fighter tank fighting waves of NR-N99 Persuader-class droid enforcers, Single Trooper Aerial Platforms, Ground Armored Tanks, Heavy Artillery Guns, IG-227 Hailfire-class droid tanks, OG-9 homing spider droids, Armored Assault Tanks, Dark Acolytes, and Protodekas.
- Grey DeLisle - Padmé Amidala, Bera Kazan
- Mat Lucas - Anakin Skywalker
- Corey Burton - Battle droid scout, CountDooku
- André Sogliuzzo - Clone trooper, Cydon Prax
- Frank Welker - Outpost Commander, Wookiee
- Lori Tritel - Luminara Unduli
- Terrence Carson - Mace Windu
- Jonathan Love - Obi-Wan Kenobi
- Charles Dennis - Ulic Qel-Droma
- Tom Kane - Yoda
- Daran Norris - Dark Acolyte, Engineer