Alright, I should know this, but how exactly does Order 66 work? When ROTS first came out the idea commonly heard was that the clones had been deep programmed to kill the Jedi when triggered, i.e., they had no choice in the matter. The scene pointed out much of the time was Cmdr. Cody firing on Obi-wan seconds after having a conversation with him with no hesitation. Subsequent books went out of their way to establish tension between clones and Jedi -- not all of them -- but there nonetheless. Jedi were often regarded as poor generals or diplomats working as a military branch. Clones were mistreated or seen as less than sentient beings since they were just clones. Then the Clone Wars TV show went through great lengths to show the clones as individuals. Jedi were shown with friends who were clones. Books basically set up an idea where the clones have free will but follow the order, so effectively is it spread without question. This gains weight from the general animosity shown between clones and Jedi, leading them to be saddened or surprised but nevertheless believing it. In some books there is even an incident where a squad of clones refuses the order, warns their Jedi general to flee, and are then collectively executed by Vader.
However, I just watched the early episodes of season 6 of the Clone Wars though and they have a great episode arc addressing this. A clone trooper named Tup straight up executes a Jedi in the middle of a battle and then tries to kill other Jedi, muttering "a good soldier follows orders" all the while. Other clones are shocked and everybody, Jedi and clones alike, assume he is either brainwashed or infected with something the Seperatists designed. He is then taken to Kamino where another clone, Fives, helps discover that he has a tumor. Unbeknownst to him and Shaak-Ti though, the Kaminoans report to Dooku that a clone has triggered Order 66 prematurely. Eventually the Chancellor shuffles some paper work so the truth is never found but this returns Order 66 to the realm of programming.
So what is Order 66 exactly, programming or effective conspiracy that plays on prejudices? I've always thought the tension between Jedi and clones seemed somewhat forced in the books. As Jedi they should care for the living regardless so the general atmosphere of them neglecting clones or treating them as lesser beings seems like a cheap plot device that goes contrary to their fundamental character. What say you?
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**[i should note that season 6 of TCW is great, it also has an episode arc where Qui-Gon speaks to Yoda and instructs him on how to retain his spirit upon his death -- setting up the scene where Yoda tells Obi-Wan that his old master has learned to commune with the living from the dead at the end of ROTS. Yoda, in his trials, sees his deepest fears (the Jedi Order falling) and is told by the Force that the dark side is closing in. Odds are the light will not survive and the only chance the light has is for its learned masters to commune with the living after their death, so efectively will the Jedi Order be wiped out. Yoda learns this but keeps it secret since he is obviously working to prevent it but is depicted as resigned to this end earlier than expected. It adds great depth to the transition to ANH and I like it. Peoples should check it out.]**