Invasion in peril! Republic forces struggle to take Umbara, a hostile planet completely enshrouded in darkness. Jedi General Pong Krell and Captain Rex lead a battalion against a constant attack by a brutal enemy. Krell's aggressive and reckless strategies backfire, killing many clones. Despite the Jedi general's dangerous tactics, Captain Rex's squad successfully captures a critical airbase. This further fuels the mistrust of Krell's leadership, dividing his men.

Knowing how essential the airbase is to the Umbaran campaign, General Krell orders it locked down as securely as possible. He receives a transmission from Obi-Wan Kenobi with bad news. The Umbaran long range missile attacks continue. Although Krell was successful in capturing the airbase, the Umbarans have rebuilt their supply lines from an orbital ship. The Separatist fleet protecting the supply ship outnumbers the Republic vessels.

Kenobi's transmission fragments into static. The Umbarans are jamming all broadcasts. Krell decides to continue with the push towards the capital, regardless of the threat of the enemy's long range missiles. Rex disagrees with this course of action, but orders are orders. The 501st battalion is to move out in 12 hours.

The veteran clones don't take the news well. Fives and Jesse characterize their orders as yet another suicide mission. Young trooper Dogma springs to Krell's defense, however, trying to convince his brothers that Krell must have a more complete picture and the experience to craft tactics that they simply don't understand.

Rex's dilemma is that he doesn't have any better alternative than an attack on the capital, but Fives has a plan. He and the other clones have examined and cracked the access codes for the captured Umbaran starfighters. With an Umbaran ship broadcasting the right signal, the clones can slip right through the Separatist blockade and destroy the supply ship.

Rex takes Fives' proposal to General Krell, who rejects it. Krell doesn't have faith in the clones' ability to pilot the alien starfighters. He needs all the foot soldiers he can to take the capital, and cannot afford to risk troopers on "frivolous adventures."

In the hangar barracks, Rex breaks the news to Fives, Tup and Jesse. Fives intends to continue the plan regardless of orders, but Rex warns that he is risking a court-martial. The clone troopers hush up when trooper Dogma enters the barracks, as they are distrustful of the younger, fervently loyal clone.

Fives continues his argument with Rex outside the barracks. Fives will not follow orders he knows are wrong. Rex counters that it is not their call -- honor and service are the hallmarks of a clone trooper. "We are part of something larger," reminds Rex. "We are not independent of one another." Fives storms off.

Back in the hangar, Hardcase attempts to pilot one of the captured starfighters. The ultra-sensitive controls require much more finesse than Hardcase is capable of, and his fighter flops about. Hardcase even accidentally triggers the fighter's laser cannons and missiles, drawing the attention of a furious General Krell. Hardcase and Fives cover for the reckless piloting, claiming to Krell it was the result of an alien booby-trap encoded within the starfighter.

Krell grounds the starfighters for being too dangerous. Hardcase, though, thinks he has the hang of flying them. Fives hatches a plan to defy Krell's orders, and pilot the fighters into the hangar bay of the enemy supply ship. There, the clones can target the supply ship's main reactor, much like Anakin Skywalker did over a decade ago during the Battle of Naboo.

Fives, Jesse and Hardcase are up for the assault on the supply ship. Fives informs Captain Rex that he is undertaking the forbidden mission. Rex knows he cannot talk Fives out of this breach of military protocol. Rex tells the ARC trooper that he cannot cover for Fives once Krell finds out.

That night at the barracks, trooper Dogma wakes up to find Jesse, Fives and Hardcase missing from their bunks. He begins to suspect they are being insubordinate. Dogma wakes Tup, but Tup doesn't say a word about the missing troopers' activities. Dogma feels obligated to report his suspicions to General Krell, and an uncertain Tup accompanies him.

Jesse, Hardcase and Fives sneak into the hangar bay and liberate a trio of Umbaran starfighters. They quickly get the hang of piloting the advanced craft and blast off into the skies of Umbara.

Despite his word to Fives, Rex covers for the fighter launch, telling Krell it was a recon mission that he authorized. Rex then intercepts Dogma and Tup before the troopers can confer with Krell.

The fighters emerge from the darkened atmosphere into the space high over Umbara, where a massive space battle between Separatist and Republic forces blazes. The trio of stolen fighters flies past the Separatist vessels, allowing the clones to fly toward the massive supply ship.

The fighters infiltrate the supply ship's hangar, weaving deeper into the enemy ship. The battle droids are prepared, however, and activate deflector shields to protect the exposed reactor core. The starfighters are now trapped inside the vessel!

Hardcase refuses to give up, and comes up with a crazy plan. The shields may stop a starfighter, but a single clone can sneak through a service door. He exits his fighter, and physically walks over one of the fighter's missile pods through a small hatch into the reactor chamber. Hardcase sacrifices himself, pushing the missile into the reactor, causing a chain reaction of explosions.

Fives and Jesse fly their swift fighters back out the hangar bay, narrowly outracing the explosion that consumes the supply ship. The blast lights up the heavens, and can even be seen from the murky surface of Umbara. With the supply ship destroyed, the capital can is no longer be heavily defended.

Fives and Jesse return, but not to a hero's welcome. General Krell is livid at them for disobeying orders. Rex tries to claim responsibility, but Fives insists that he be punished, for it was his idea. Krell cares little for such displays of honor. The angry Jedi orders Fives and Jesse to be court-martialed and executed. "Make no mistake. For crossing me, you will pay the price," says Krell.