Jedi Knight Anakin Skywalker and Jedi Master Obi-Wan Kenobi lead Republic forces in an attempt to defeat the droid armies and free the planet of Christophsis from the Separatist siege. When the Republic is ambushed and forced to retreat, it becomes clear that someone in their midst has set them up. The Jedi believe this infiltration is a Sith-backed operation and go behind enemy lines to investigate. Meanwhile, Captain Rex and Commander Cody set out to uncover the traitor amongst them.

Note: This episode takes place between episode 2x16 ("Cat and Mouse") and the feature film

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!