WARNING: The following contains spoilers for the Star Wars: The Clone Wars Season 7 episode "Shattered," streaming now on Disney+.
The penultimate episode of Star Wars: The Clone Wars finally syncs up with the moment Chancellor Palpatine issues the dreaded Order 66 in Revenge of the Sith, and turns the clone army against the Jedi. While fans get to see Ahsoka Tano fight for her life aboard a Republic Star Destroyer, we also learn the directive extends beyond the Jedi when it comes to targets.
While the starship is in hyperspace, Captain Rex and Ahsoka share a quiet moment before the clone trooper is called away for an important briefing. It's here that Anakin Skywalker's turn to the Dark Side is heard by Ahsoka, culminating in Darth Sidious (Palpatine) giving Order 66 to Rex. After Ahsoka barely escapes the clones' initial attack, Rex's first order is for a squad to go to the detention level to execute the captured Maul, who is definitely not a member of the Jedi Order.
That possibly means the Order 66 instructions directed at Rex in The Clone Wars are slightly different than the one heard in Revenge of the Sith. Of course, there is a logical explanation for why Sidious would order Maul's execution. As Sidious' former apprentice, Maul is an obstacle to the soon-to-be Emperor achieving his galactic goals. Part of Maul's plan during the Siege of Mandalore involved luring Obi-Wan Kenobi to the planet to reveal how Palpatine has secretly been grooming Anakin as his new apprentice. However, because Ahsoka arrived on Mandalore instead of Obi-Wan, Maul was forced to divulge the details to her, resulting in a fight and his capture.
After the clone troopers leave to execute Maul, Rex gives additional orders to execute the Jedi leadership for treason against the Republic, adding, "Any soldier that does not comply with the order will also be executed for treason." Although it's unclear what other "Jedi leadership" Rex is referring to, that's an odd order to give to clones with inhibitor chips in their skulls. The chips are what Palpatine uses to turn the clones against the Jedi, so there shouldn't be any worry that they would go against his directives. However, as Rex shows when he attacks Ahsoka, there are flaws in the plan.
While Rex points his blasters at Ahsoka, his hands visibly shake. Rex even gives her a clue when he keeps referring to Fives, another clone who discovered an issue with their chips in Season 6. Fives died before he could pass on the vital information, but Rex left an encrypted message documenting his reservations, which Ahsoka found. Along with this information -- and three droids -- she is able to trap and knock out Rex. Once unconscious, Ahsoka uses the Force to locate Rex's inhibitor chip, allowing a droid to deactivate it and bring him back to his senses.
These new revelations make it clear Sidious was aware his clone army could be compromised, although the number to actually pull it off would be very low. Outnumbered, any turncoats would surely be executed on the spot, so the likelihood of any escaping is minimal. There is only one episode left in The Clone Wars to learn how Captain Rex and Ahsoka Tano escape the clutches of the Republic.
Streaming on Disney+, the final season of Star Wars: The Clone Wars stars Matt Lanter as Anakin Skywalker, Ashley Eckstein as Ahsoka Tano, Dee Bradley Baker as Captain Rex and the clone troopers, James Arnold Taylor as Obi-Wan Kenobi, Katee Sackhoff as Bo-Katan and Sam Witwer as Maul.