Rex struggled to fulfill Order 66 in Star Wars: The Clone Wars, unlike his clone brothers. In the final two episodes of the series, the moment fans waited for finally arrived. By indirectly overlapping with Star Wars: Episode III- Revenge of The Sith, the animated series covered the commencement of the largely successful Jedi purge. The ever-committed clones carried out the gruesome command with no second thoughts — except for at least one. Rex tries his hardest to combat his nature before inevitably failing to think independently. His hesitation is not without reason, hence why he is the only one to do so.
Following the apprehension of Darth Maul, Rex and Ahsoka Tano depart from Mandalore. Their task is to deliver the Sith Lord to the Jedi Council back on Coruscant to answer for his crimes. Their voyage goes smoothly until the latest transmission arrives, delivered by Darth Sidious himself. He tells Rex to execute Order 66, meaning he must eliminate his Jedi general and those who protect her. Sensing something is wrong, Ahsoka steps into the middle of a trap, being held at gunpoint by her once ally.
There is an intense staredown as a trembling Rex urges Ahsoka to stay back. His ability to speak becomes impaired as he tells her to find Fives before giving in and opening fire. The entire scene is a fresh take on Order 66, hinting at the clone's autonomy or lack thereof for the first time. His resistance to the order is unlike anything seen from them in previous Star Wars media. The clones are consistently depicted as cold-blooded killers once Sidious gives them their assignment. Rex is something of a special case, whose unsuccessful attempt to fight his programming is an anomaly. However, it is by no means a mystery as there is an explanation for his erratic behavior.
The file he begs Ahsoka to find is telling in regards to his reluctance to complete Order 66. It is on a clone named Fives, and within the folder is a recording of Rex talking about their inhibitor chips. He explains his worry over them and the power they possess if in the wrong hands. As Order 66 depicted, he realized his worst fears about the implants, which erased all clones' free will. Its influence on his mind is unbreakable, but his attempt to resist it is a result of his awareness. Rex understood what the chips were capable of, so he fought a mental battle over his thought process.
Thankfully for him, Ahsoka removed his chip before he could harm or even kill her. Rex knew for a long time how shady the implants were, but he didn't say a word since no one would listen. After the Clone Wars ended, Rex lived an incredible life on his terms. He experienced an autonomous life other clones never knew, as they remained loyal to the Empire for years. In the end, his suspicions of the inhibitor chips saved both his life and Ahsoka's. The Clone Wars was bound to end with Order 66, but that didn't mean Rex needed to become a slave to his programming.