« Reply #25 on: August 12, 2010, 08:12:57 pm »
My take, based on the movie alone, as I haven't seen the much of the cartoon or read the book, is that Order 66 was one of a series of contingency plans that Palpatine put in place to further cement his rule over the Republic after the army was created. I'd be willing to bet that a series of Orders were set up to order the deaths of prominent senators, or even the entire senate. And others would have been set up to kill various members of the Jedi Council, or all of them, but leave the rest of the order intact to be corrupted at the Sith lord's leisure. The planning required would be quite impressive, probably involving years of effort and deceit, only to culminate in a few keystrokes and a brief holonet message sent to the various clones involved.
Given the characters involved, I would guess that Palpy used a series of deep conditioning drugs, hypnotic suggestions, and possibly an unknown sith techniques, delivered by a series of secret agents in the army's medical corps, delivered to those clones that he felt he could count on to follow the orders of those who were directly involved in his plans, or also conditioned to obey his order to murder their commanders. Rex, from what I know about him, would not have been included in Palpy's scheming, assuming he was alive at the time Order 66 was put into effect. I don't know as much about Cody, but he was apparently more amenable to taking Palpy's orders, or at least to killing Obi-Wan and the other Jedi.
And to add another wrinkle or two (no pun intended), how did the newly disfigured Palpy not get challenged by the troops he gave the order to? Even with the hood up on his robe to hide his face, his voice sounds different, and it's a fair assumption that a voiceprint ID would fail. The only explanation I have is that the computer added some sort of authenticator codes to the outgoing transmission that were accepted by the individual trooper's communicators and passed on to the troopers.