While fighting to control the darkened world of Umbara, Anakin Skywalker's battalion is temporarily placed under the command of Jedi General Pong Krell. As Krell's disastrous strategies result in increasing casualties, his men begin to turn against him. Captain Rex struggles to balance loyalty between his commander and his fellow men. Under his watch, Fives and Jesse disobey Krell's orders, resulting in their court-martial.

Captain Rex tries to reason with Krell, but the general has made up his mind. He sees the insubordinate clones as defective and as a bad example to the rest of the battalion. As time is short, Krell orders Fives and Jesse executed immediately.

Rex, Sergeant Appo and several other clones release the prisoners from the brig to be executed. Rex explains their fates, and Fives stoically accepts responsibility for his actions. Jesse is stunned by Krell's callous orders, and Fives warns Rex that Krell has been using him to ensure the loyalty of the troops.

At the landing pad of the airbase, Jesse and Fives are marched up against a wall by their fellow clones. Trooper Dogma commands the execution. Fives pleads one final time for the clones to come to their senses. Much to Dogma's surprise, the firing squad refuses to go through with the order. Dogma insists that the troops follow orders, but Rex overrides him, and has Fives and Jesse freed from their binders.

Rex and Dogma's report to Krell on the failed execution is interrupted by a transmission from the battlefront. Waxer, a clone from Kenobi's battalion, describes an Umbaran attack that has seized a supply of clone armor and weapons. The Umbarans are gearing up for a massive attack. Krell orders Jesse and Fives locked up. The matter of their punishment is postponed, not finished.

Rex leads the forward platoon through the briar fens of the Umbaran wilderness. He warns them to stay alert, since the Umbarans may use the captured Republic supplies to create confusion.

Trooper Tup stops Dogma from blundering his way onto a vixus' vine-like tentacles. Tup demonstrates the danger by dropping a rock onto the vixus' mouth. It snaps awake and thrashes its tentacles, looking for prey.

Suddenly, blaster bolts rain in from the darkness. The 501st clones scramble for cover. Rex orders the mortar troopers to fire. Kix's night vision goggles make out the targets: the Umbarans have indeed captured Republic armor -- they're disguised as clones of the 212th.

As Rex rushes through the battlefield he makes a horrible discovery. Unmasking a fallen enemy, he sees not the face of an Umbaran -- but the face of a clone! Rex frantically calls out to the battlefield, ordering his troops to remove their helmets so the other troopers can see they are not enemies. The soldiers are shocked to discover they have attacked and killed their brothers.

Kix finds the dying platoon leader from 212th -- Waxer. With his final breaths, Waxer reveals to Rex that it was General Krell who ordered the attack. He supplied the coordinates for the battle, and told the 212th that the enemy would be arriving in captured armor.

Captain Rex gathers the survivors of his platoon. He informs them that he is about to undertake a mission that can be seen as highly treasonous -- he is going to arrest General Krell for treason against the Republic. The troopers stand with him, though Dogma is conflicted by these orders. Rex returns to the airbase and frees Fives and Jesse from the brig.

Rex and the troops storm into the airbase command center and order Krell's surrender. Krell doesn't explain his actions; instead, he remains contemptuous of the clones. He ignites his lightsabers and slashes through the troopers, then leaps from the airbase tower and runs into the forests.

Rex and the troopers give chase, but are stopped by Dogma. The uncertain trooper tries to remain loyal to the general. "I used to believe that being a good soldier meant doing everything they told you," says Rex. "That's how they engineered us. But we're not droids. We're not programmed. You have to learn to make your own decisions." Dogma lowers his weapons, and the clones continue their pursuit.

In the thick of the briar fen, Krell slashes through the pursuing clones, cackling with dark glee all the while. Tup has an idea, and suggests that Rex lead Krell towards him.

Tup lures Krell toward the dormant vixus. In his eagerness to cut down the clone, Krell wakes the beast. The monstrous creature wraps Krell in a tentacle. Though the Jedi can cut his way free, the vixus pins him long enough for Tup to blast him with a stun ray.

Krell is now shackled in the brig. Rex confronts the fallen general, and Krell reveals that he has strayed from the Jedi path for he has seen the future: the Jedi are going to lose the war and the Republic will be torn apart from within. A new order will rise to replace it, and Krell intends to survive and rule as part of it.

Krell has been attempting to curry favor with Dooku by driving the Republic from Umbara. Dogma is aghast at Krell's treachery. The cruel Jedi used Dogma's loyalty to get his way. Krell intends to simply wait out the Umbaran counterattack, confident that they will recapture the airbase and free him.

Sergeant Appo reports to Rex that though Obi-Wan's forces have conquered the capital, the fleeing Umbarans are heading toward the airbase. Time is running out. Fives refuses to allow Krell to be captured by the enemy. He knows too much. He's too dangerous to be taken alive.

Rex returns to the brig. He must execute Krell, but he finds it difficult to kill to an unarmed Jedi by shooting him in the back. Krell savors Rex's hesitation. A shot rings out and pierces Krell's heart, but it did not come Rex's blaster. Dogma holds a weapon lifted from Fives' holster. "I had to," exhales Dogma. "He betrayed us."

The Republic has secured Umbara. It is a victory, but Rex does not feel like celebrating. He wonders what the point of the war is. And what happens to the soldiers when it ends?