Jedi Master Kit Fisto and his former Padawan, the Mon Calamari Jedi Nahdar Vebb, track escaped prisoner Nute Gunray to a remote world. Following Nute into a mysterious den filled with strange creatures, weapons, and war-time artifacts, the Jedi discover it is the trap-laden lair of General Grievous! Learning that Count Dooku has led the Jedi there in order to punish Grievous for his recent failures, the General is determined to prove his abilities and destroy the Jedi. Kit and Nahdar, along with a contingent of clones, must now fight their way past Grievous and his caretaker droid A-4D to avoid being caught in General's evil clutches forever.

Medical supplies are desperately needed for a crucial Republic battlefront. While the Jedi Knights transport Poggle the Lesser as a prisoner to Coruscant, the Padawans Barriss Offee and Ahsoka Tano are dispatched to escort the medical frigate to its destination. When Geonosian brain worms take control of the clone troopers aboard their supply ship, Ahsoka and Barriss must battle to stop the vessel from unleashing the deadly plague upon the galaxy.

Anakin Skywalker and the rest of his Jedi team have been overrun by the Separatist surprise attacks led by Riff Tamson while Prince Lee-Char and Ahsoka must evade capture on their own. Unable to summon more Republic aid, Yoda calls upon the help of the powerful and amphibious Gungan Grand Army, but whether they will be enough to stop the Separatist siege is uncertain. An incensed Tamson doubles his efforts in tracking down Prince Lee-Char, unleashing the reinforcements given to him by Count Dooku in an assault that churns the oceans.