The Hidden Enemy

As Anakin and Obi-Wan strive to guide Republic forces in liberating Christophsis from a Separatist siege, they stumble upon indications of a traitor lurking within their ranks. The Republic's ambush on Christophsis reveals a setup, prompting Jedi suspicion towards the Sith. Meanwhile, Rex and Cody uncover intelligence suggesting the presence of a spy among them.

Anakin, Obi-Wan, along with their clone troopers, are getting ready to spring an ambush on the approaching droid forces from a pair of towers that overlook the droids' route. Just as they're about to unleash their attack, the droid formation unexpectedly splits into three columns, and droids materialize in Obi-Wan's building. Anakin promptly requests a gunship for immediate extraction before leading his squad to assist Obi-Wan. They make their way to the roof to escape, but the droids pursue them. Their gunship arrives and retrieves them, but only after they manage to grab the head of the command tactical droid's in an effort to discover how the Separatists learned of their strategy.

Back at the base, Rex and Cody begin analyzing the droid's memory banks; however, the most they can extract before the droid head fries is confirmation that the Separatists had prior knowledge of their location. Obi-Wan raises the possibility of a spy within their own ranks. The Jedi determine that they will infiltrate enemy territory to investigate, instructing the clones to keep the mission a secret. As the Jedi depart, Cody notices someone's comlink was left on, allowing them to overhear their conversation. Rex and Cody notice a figure fleeing the scene and give chase. Regrettably, they lose the suspect in the mess hall, surrounded by their fellow clones, indicating that one of them is a traitor. They decide to contact the Jedi, but communications are being jammed by droids.

To uncover any unauthorized transmissions, Rex and Cody task R2-D2 with analyzing the communication logs. Rex detects an unusual wavelength, too weak and infrequent for typical detection. The signal appears to originate from Slick's barracks, prompting an investigation. They interrogate each of Slick's men: Jester was occupied with cleaning his weapon, Punch and Sketch were in the mess hall, and Gus was receiving treatment in the infirmary. The last one, Chopper, seems to be hiding something, and reluctantly reveals that he was amassing droid fingers as war trophies, a violation of protocol. Chopper denies being a spy, and Slick suggests a thorough investigation upon the Jedi's return.

Nevertheless, Chopper blurts out that he witnessed Slick entering the command center instead of the mess hall, and Cody points out that Slick is somehow aware of the Jedi's departure. Slick, realizing he's been exposed, makes his escape. Cody and Rex pursue him, but they're too late: Slick detonates previously planted explosives, destroying the majority of the gunships, AT-TEs, and the weapons depot. The other clones inform Cody and Rex that Slick went into the command center, and they order the others to secure the perimeter while they go inside.

Meanwhile, as Anakin and Obi-Wan speed toward the Separatist base on BARC speeders, they spot a growing number of droids observing them, but they decide to proceed with the mission, even though it's been compromised. Upon reaching the enemy base, they encounter Asajj Ventress once more and engage in a duel. The Jedi gain the upper hand over Ventress and demand her surrender, but as they move in to capture her, she uses her lightsabers to create a large hole in the floor beneath them, dropping them to a lower level. Ventress mocks them and flees, and the Jedi give chase, only to discover that she has prepared an entire army to invade Christophsis. The Jedi battle Ventress again, destabilizing the tri-droid she is standing on before escaping on STAPs. Ventress instructs General Loathsom to deal with the Jedi while she advances to the next stage of her master's plan, heading toward the Trident.

Rex and Cody enter the command center, searching for Slick. They quickly deduce that he's hiding in the ventilation system and subtly stage a scene: Cody leaves his blaster on the table while Rex goes to "secure the lockdown." Slick emerges from the vents and grabs Cody's blaster, only to find it's unloaded, and Rex appears from behind him. Slick engages the commander and captain in hand-to-hand combat, revealing that he was weary of the constant suffering and was offered freedom and payment by Ventress. Cody manages to subdue him, and they apprehend him. As they present Slick to the Jedi, Slick declares that his brothers are enslaved by the Jedi, that his actions were a blow for all clones, and that he loves his brothers, but Cody and Rex retort that he has now doomed them all.

Cody instructs the other clones to escort the traitor to the brig. Rex reports that despite the destruction of most of their weaponry, they managed to salvage the heavy cannons, which will be invaluable in the upcoming battle.

The initial script included a scene where the clones were setting up a combat droid called "The Beast," similar to the dome-shaped mining droids seen in A New Hope. However, this scene was removed to maintain the focus of the war as clones versus droids, rather than clones using droids against droids, and because the scene didn't clarify the droid's purpose.

At the episode's beginning, Cody is seen carrying a plain white clone helmet upon returning with Slick. Later in the episode, he is shown wearing his proper helmet.

During Obi-Wan's explanation of the Jedi's mission behind enemy lines to Cody and Rex, he mistakenly refers to Cody as "Captain" when Cody is clearly a Commander. This error occurred during editing because Obi-Wan was originally addressing Rex. Additionally, before Cody and Rex speak with Slick's men, Slick says, "Captain, give me just a moment with them..." Cody then turns and looks at Slick.

During the episode, Chopper's right eye changes color. Initially, when he is suspected, his right eye matches the brown color of his left eye. However, later on, his right eye appears as an off-white color.

Much of the background music consisted of an edited version of the "Battle of Christophsis" track from The Clone Wars film soundtrack. Furthermore, the music accompanying the fight between Rex, Cody, and Slick is a variation of the speeder chase music from Attack of the Clones.

The Hidden Enemy was broadcasted on September 16, 2012, on Atlanta's MyNetworkTV, preceding a televised showing of Revenge of the Sith.

When Kenobi, Skywalker, Cody, and Rex are examining the tactical droid's severed head, the word 'tactical' is written in Aurebesh on the side of the droid's head.