When Anakin is forced to temporarily turn over command of his clone troopers to a new commander, the Jedi Pong Krell, tensions begin to run high as the clones are assigned with a very deadly mission to take the capital of Umbara.

General Krell orders Captain Rex and the clone troopers of the 501st Legion to conquer a heavily fortified Umbaran airbase, and will not accept anything less than victory. It is an almost certain suicide mission, unless the clones can use their ingenuity to defeat their new enemy.

After the Republic conquers an Umbaran airbase, General Krell orders Rex and his men on towards the heavily fortified capital. Realizing there's a better plan, several clone troopers disobey orders to carry out a rogue, covert operation.

With two of his men facing execution for disobeying orders, Captain Rex must confront his overly aggressive commander, General Krell. Risking charges of mutiny, Rex must make a dark choice as the true face of the enemy emerges.