Because Star Wars: The Clone Wars was created after the prequel trilogy, part of the main focus of the series was bridging the gap between Star Wars: Attack of the Clones and Star Wars: Revenge of the Sith. While many episodes support this goal, one of the most subtly revealing episodes is "Brain Invaders" from Season 2. In the episode, Geonosian brain worms infect the Clone Troopers aboard a medical supply ship, and the clones' actions while infected hint at their inhibitor chips and their deadly programming under Order 66.
The brain worms were introduced in the previous episode, "Legacy of Terror." The Geonosian Queen Katrina the Great uses the worms to infect dead Geonosians, creating a zombie army. She shows that she can infect the living, too, when she kidnaps Jedi Master Luminara Unduil. The Jedi rescue Luminara and collapse Katrina's temple. They believe that the matter is solved, not realizing that some of the brain worms survived.
In "Brain Invaders," some of the brain worm eggs hatch and infect the Clone Trooper Scythe before he boards a ship assigned to pick up medical supplies for the Republic army. This mission, led by Padawans Ahsoka Tano and Barriss Offee, seems simple on the surface, but it becomes far more dangerous as Scythe quickly infects the rest of the clones. Ahsoka and Barriss discover the Geonosian brain worms' plot, and they must both warn the rest of the Republic and try to make sure no one else is infected. They split up, noting that it is a bad idea, but they have no other choice.
When the Clones Troopers corner Barriss, one of the infected Clones states that "If there's one thing we clones know, it's how to stop a Jedi." Within the context of the series, this line seems nonsensical; the Clones, with one notable exception, have been firmly on the side of the Jedi. Instead, the brain worms have accessed the parts of the clones' brains that contain Order 66 and the knowledge that the clones will need to execute the Jedi on Palpatine's command. The Clone Troopers also show that the statement is true; Barriss stumbles into their trap, and the clones infect her as well.
The ship is saved because the Jedi discover that the brain worms die in extreme cold, but the method through which this information is obtained is also morally questionable. Anakin Skywalker interrogates Poggle the Lesser, Queen Katrina's advisor. When Poggle refuses to talk, Anakin attacks him, and in the process, Anakin uses the Force to choke Poggle. This is not the first time that Anakin uses the Force for torture, but this specific method of torture is similar to tactics he would use later as Darth Vader. Thus, the episode also foreshadows Anakin's fall to the Dark Side.
Perhaps even more chilling, though, is a line from earlier in the episode. On Geonosis, when Pulsar, one of the Clone Troopers, complains about transport duty, his commander reprimands him, stating, "We were bred to follow orders, Pulsar. You got a problem with that?" This statement is literally true, but it also shows the morally unstable ground the Jedi walk on by using Clone Troopers to fight. The Jedi are creating sentient beings to have less free will, through biology or conditioning, and the Jedi are not truly giving the Clones options or a choice of whether they actually want to participate in the war. This gray moral judgment also extends to the Jedi's treatment of their Padawans. Both Ahsoka and Barriss are young teens, and, as Barriss states, still learning, but they are already commanding missions and facing dangers far beyond their years. Thus, the episode lays more groundwork to show why the Jedi fell and how they have strayed from Jedi ideals during the Clone War.
Thus, years before Order 66 came into play, the writers of The Clone Wars start building the foundation for the events of Revenge of the Sith and the fall of the Jedi. While the episode hints at the clones' programming in their inhibitor chips, the writers also set up more complicated moral dilemmas. "Brain Invaders" calls in to question the Jedi's choices in the war and the moral problems with using the Clone Troopers and Padawans on the front lines.
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