Yoda travels to a neutral coral moon of Rugosa to persuade King Katuunko to allow the building of a Republic supply base on Toydaria. However, Asajj Ventress makes sure she arrives first to offer Katuungo a similar offer from the Separatist side.
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.
When R2D2 goes missing in action during a skirmish in an asteroid belt Anakin insists on mounting a rescue mission. Although Obi-Wan is against wasting time on a droid, Anakin explains the R2's memory has never been wiped and thus carries all of the Republic's tactics and base locations. Meanwhile, the plucky Atromech has been picked up by Trandoshan scavenger Gha Nachkt in his freighter, Vulture's Claw. Nachkt plans to sell the droid to the highest bidder.
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.