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The "white jobs" (normal clone troopers) followed the orders to the letter because they weren't given independent thinking. However, the Commandos, who were given independent thought so that they could quickly adapt to changes in the field, gained a conscience during the Clone Wars and so didn't immediately follow Order 66. Palpatine didn't program Operation Knight Fall into every clone's minds. Order 66 was part of a document that listed individual responses to act upon in the event of such a scenario occurring. Order 66 claimed that in the event of the Jedi no longer serving the Republic's best interest and planning a coup for power, they must be eliminated. On that document were other such responses as the Chancellor refusing to step down, or the Senate rebelling the Chancellor's decisions. It was just a selected scenario for the clones to follow. Also, the few Commandos who rebelled and went into hiding faced the same outcome as the Jedi. If any were discovered, they would be labeled as traitors and would be killed.

Normal clones DO HAVE independent thinking- even most droids do- but they are modified to be ultimately loyal to the Chancellor if order 66 is given- not all commandos rejected that order so there is not so clear difference between commandos and normal clones- also republic commando novels do have canonical inaccuracies so they shouldn't be taken as only source...

http://starwars.wikia.com/wiki/Order_66#Execution_of_the_Order

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