With the help of his Padawan Ahsoka and Jedi Master Plo Koon, Anakin utilizes new long-range Y-wing bombers to lead a bold strike on General Grievous' warship, the Malevolence, and its destructive weapon.

In the sterile laboratories of Kamino, the ailing clone trooper Tup and his friend ARC Trooper Fives are quarantined for examination following Tup's shocking murder of a Jedi Master. With the help of medical droid AZI-3, Fives is determined to get to the bottom of Tup's condition and uncovers a secret buried deep within the Republic's cloning program.

The body of clone trooper Tup is scheduled for transport to Coruscant, where Chancellor Palpatine's own doctors will closely examine it. ARC Trooper Fives breaks protocol and defies orders to dig up answers, and discovers that there is an organic construct of unknown purpose hidden in the brains of all clone troopers.

Maul is captured and the Siege of Mandalore is won. But evil lurks elsewhere, and the galaxy will never be the same.