The Republic discovers a Separatist bio-weapon lab hidden on the planet of Naboo. Rather than wait for help, Padmé; explores the lab with Jar Jar. Anakin, Ahsoka, Rex, and Obi-Wan arrive and follow after her. They find that the Senator is being held captive by the sinister Dr. Nuvo Vindi. The mad scientist has been developing a lethal virus for the Separatists. Vindi threatens to set off a bomb and release the virus!

Even though the lab has been shut down, Dr. Vindi manages to activate the dreaded Blue Shadow Virus, infecting Ahsoka, Padmé, and many clone troopers. The plague is fatal within 48 hours. Anakin and Obi-Wan must travel to the mysterious planet, Iego, to secure the only known antidote to the sickness. Anakin and Obi-Wan arrive on the mysterious planet to find its population living in fear of a mysterious force that has been killing anything that tries to leave their world. With the help of Jaybo Hood, a clever Iegoan boy, Anakin and Obi-Wan must solve the planet's mystery before they can leave, and before everyone infected with the Separatist virus dies!

Cad Bane has stolen a Jedi holocron which holds the secret locations of the galaxy's Force-sensitive children. Bane is tasked by Darth Sidious to kidnap several of the children to train as Sith spies. On one such kidnapping attempt, Bane is captured by Anakin and Ahsoka and brought before Obi-Wan and Mace Windu to have his mind probed. Unable to resist the combined Force powers of the Jedi, Bane agrees to lead Kenobi and Windu to his hidden base while Anakin and Ahsoka venture to Mustafar to save the stolen children from Darth Sidious' evil plot.

Back on Coruscant, Clovis -- known traitor of the Republic -- makes a dubious deal which puts him at the head of the Banking Clan. Anakin's increasing distrust and hatred of Clovis strains his relationship with Padmé to the breaking point.