Order 66 was one of many contigency orders given to the Clone Armies to train for.  What makes this different to the other orders is that it could only be given by Senator Palpatine and could not be over ruled.

Order 66 = Seek and use lethal force against the Jedi, due to an attempted coup on the republic by the Jedi. This was just an excuse for Emperor Palpatine to destroy the Jedi as his identity of being a Sith lord had been discovered.

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