Players must complete mission cards on specific planets based on certain episodes of Star Wars: The Clone Wars. The missions are represented below with the specific planet, episode, and a brief summary of the conflict.
- "" - Toydaria - "Jedi battle Separatist forces to win favor and forge a treaty with King Katuunko of Toydaria."
- "" - Alderaan - "Tenacious bounty hunter Aurra Sing makes several attempts to eliminate the key speaker of a humanitarian conference."
- "" - Kashyyyk - "Separatists launch a large-scale invasion of the Wookiee homeworld, targeting the planet's oil refinery."
- "" - Naboo - "In a secret bio-weapons lab, Dr. Nuvo Vindi engineers an airborne strain of a previously eradicated disease."
- "" - Rodia - "Jar Jar Binks disguises himself as a Jedi in order to rescue his fellow senator and capture Nute Gunray."
- "" - Christophsis - "A prototype stealth ship attempts a supply run as Separatist Admiral Trench blockades the planet."
- "" - Mustafar - "Jedi must rescue Force-sensitive children kidnapped by bounty hunter Cad Bane."
- "" - Lola Sayu - "A daring rescue is mounted at an impenetrable prison designed to hold rogue Jedi."
- "" - Kamino - "When a clone suddenly kills a Jedi, he is taken to the laboratories of Kamino to determine the cause."
- "" - Umbara - "General Pong Krell's reckless tactics prove deadly for clone troopers as they march to take the planet's capital."
- "" - Coruscant - "Cad Bane seizes control of the Galactic Senate Building, trapping senators and officials inside."
- "" - Nal Hutta - "When crime lord Ziro the Hutt is broken out of prison, it is up to the Jedi to track him down."
- "" - Ryloth - "The Separatists attempt to bomb the capital city rather than allow the Republic to liberate it."
- "" - Rishi - "Clones must defend a Republic listening post from attack by disguised droid commandos."
- "" - Serenno - "Undercover Jedi must survive the deadly trials of a construct designed to separate the weak from the strong."
- "" - Bardotta - "After the vanishing of several Dagoyan Masters, Queen Julia requests aid, though she is wary of Jedi involvement."
- "" - Mandalore - "Jedi investigate rumors concerning Duchess Satine Kryze and run afoul of the Mandalorian terrorist group Death Watch."
- "" - Oba Diah - "Following the trail of Master Sifo-Dyas, the Jedi discover a lead: a forgotten captive of the Pyke Syndicate."
- "" - Malastare - "When a weapons test awakens a colossal creature from beneath Malastare, the Republic must find a way to contain it."
- "" - Onderon - "The Jedi secretly aid a rebel cell led by Saw and Steela Gerrera as they resist Separatist rule of their homeward."
- "" - Anaxes - "Jedi attack a Separatist dreadnaught and droid assembly plant in a coordinated effort to retake the planet."
- "" - Mon Cala - "When the king is murdered, the Quarren and Mon Calamari are thrown into conflict, spurred by Separatist influence."
- "" - Geonosis - "While Separatist super tanks engage a frontal assault, Jedi launch an incursion through Geonosian catacombs."
- "" - Dathomir - "After a savage attack on a temple, Jedi visit the Nightsisters of Dathomir to search for the killer."