Here we learn that Ahsoka and Rex refused to kill any of the Clones trying to murder them, and that Maul jacked the shuttle they intended on using to escape. She had to use the Force to find the chip, as scans wouldn’t reveal its location in Rex’s head, but once it was found the chip was removed and Rex no longer wanted to murder Ahsoka, so she now had an ally for her escape, which picks up in episode 12, “Victory and Death”. With that knowledge, she used those same droids, R7, Cheep, and GG, to knock Rex out and get him to a med bay to have the chip removed. It all starts in “Shattered”, where we learn that Ahsoka used some Droids to first learn about the inhibitor chips that Five warned Rex about back in Season 6. After all, they didn't kill him and somehow he was able to climb out of the pit and escape in a stolen fighter without the clones noticing.Thanks to the final two episode of The Clone Wars’ seventh season, we now have a definitive answers as to how Ahsoka Tano and Captain Rex survived Darth Sidious’ Order 66.
You could also argue that Commander Cody or his gunner may have disobeyed orders to some extant when they fired on Obi-Wan riding his Boga. Several clone commando units (Omega Squad and Delta Squad) also disregarded the order, and Captain Maze not only didn't execute Jedi Arlingan Zey, but helped to smuggle him into exile (novel: "Order 66: A Republic Commando novel") (From the novel "Dark Lord: The Rise of Darth Vader") Ion Team, a group of clones that were close with their assigned Jedi, refused the order on the grounds that it was not valid - they believed it was a false enemy signal, and helped protect their Jedi against their fellow clones. There were a few clone troops that disobeyed the order: Most of the clones did follow Order 66 and killed their Jedi generals.
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