General Grievous uses his latest weapon , the Malevolence to destroy Plo Koon's fleet. Stuck in an escape pod with three Clone troopers, Koon fends off more battle droids while Anakin and Ahsoka mount a rescue mission.
Padmé Amidala and C-3PO fly into a trap and are taken hostage by General Grievous aboard the Malevolence. Anakin and Obi-Wan, who were already in pursuit of Grievous, now have to board the ship in order to rescue the senator and her protocol droid.
A squad of rookie Clone Troopers manning a tracking station on the Rishi moon is attacked by a new model of commando droids. Commander Cody and Captain Rex arrive just in time to aid the Shinies in taking back their base - the last outpost before their 'home' planet of Kamino.
Anakin and Ashoka are ordered to destroy General Grievous' secret enemy listening post. Against Obi-Wan's wishes, Anakin makes use of the opportunity to mount a one man rescue mission to find R2-D2. Meanwhile, R2's replacement R3-S6 seems to be working against Ahsoka and Rex's squad as much as helping them.
Padmé Amidala travels to Rodia to meet with old family friend Onaconda Farr about the lack of food rations. Unfortunately Farr has just made a deal with the Separatists. Padmé is imprisoned, leaving it up to Jar Jar Binks and C-3PO to rescue her.
Luminara Unduli and Ahsoka Tano are transporting the captive Viceroy Nute Gunray to Coruscant to face trial. Count Dooku deploys his apprentice Asajj Ventress to make sure Gunray is either recaptured or killed rather than have him spill Separatist secrets.
Kit Fisto is on the trail of the recently escaped Nute Gunray and joins up with his former Padawan Nahdar Vebb on the remote planet of Vassek. Unknown to them, they are entering the lair of General Grievous, who is being tested in his abilities by Count Dooku after a series of disappointments in battle.
Obi-Wan and Anakin infiltrate Count Dooku's frigate in an attempt to capture him but all three end up crash-landing on the planet Vanqor instead. While the Jedi are busy fighting a mother Gundark, Dooku falls into the hands of a pirate gang led Hondo Ohnaka. The pirate chief then offers Dooku up for ransom to the Republic in exchange for a million credits worth of spice.
Obi-Wan and Anakin are now hostages along with Dooku at Hondo Ohnaka's stronghold on Florrum. Delegate Jar Jar Binks and Senator Kharrus arrive with the ransom and a battalion of troopers, only to find there is treason within the pirate ranks.
General Skywalker is injured while rescuing fellow Jedi General Aayla Secura from Super Battle Droids equipped with rocket packs. Ahsoka Tano crash-lands their shuttle on the neutral planet of Maridun, where the native Lurmen villagers refuse to takes sides in the war. They are however willing to send a healer to help Anakin.
A separatist fleet led by Neimodian Lok Durd arrives on Maridun to test their new defoliator weapon, which destroys organic live but leaves machines intact. Unknown to them, three Jedi and two Clone Troopers are stuck nearby without a means of transport off planet. When the Lurmen village becomes endangered by the test, the Jedi rush to defend it, despite the objections of village elder Tee Watt Kaa.
Obi-Wan, Anakin and a detachment of the 501st investigate the slaughter of a Republic outpost on Orto Plutonia. They soon find a Separatist base destroyed by the same aggressors, who turn out to be a clan of native Talz that just want to be left alone. Unfortunately Pantoran dignitary Chi Cho claims the planet to be under his people's jurisdiction and orders the unwanted aliens to be either removed or wiped out. As the Jedi cannot interfere, the only hope for a peaceful resolution lies with young senator Riyo Chuchi.
Evil scientist Dr. Nuvo Vindi is recreating the dreaded Blue Shadow Virus in his secret underground lab on Naboo. When he captures Senator Amidala and Representative Binks, Jedi Generals Skywalker & Kenobi mount a rescue operation.
The deadly Blue Shadow Virus is unleashed in Vindi's underground lab with Padmé, Ahsoka, Jar Jar and several Clone troopers stuck in it. Anakin and Obi-Wan have just 48 hours to find a cure. They travel to the moons of Iego but will have a hard time trying to get past the 'Ghost of Drol' in order to leave again.
During the battle for Ryloth, Obi-Wan, Commander Cody and his 212th Attack Battalion set out to free the occupied Twi'lek village of Nabat. Two troopers, Waxer and Boil find a young girl named Numa who becomes instrumental in Obi-Wan's plan.
Cad Bane has gathered a team of his fellow bounty hunters to seize control of the Senate Building. The plan is to exchange the hostages therein for the freedom of crime lord Ziro the Hutt. Anakin Skywalker is the sole Jedi left in the building, but unfortunately he has left his light saber in Senator Amidala's possession.