Order 66 or Clone protocol 66 was the top-secret order marking all Jedi as traitor to the Republic. For that reason, every clone trooper with an inhibitor chip followed order 66, killing most of the Jedi. The clones without the inhibitor chip however, didn’t execute order 66 and deserted the Republic. The Kaminoins who developed the clones, originally thought that the inhibitor chip was to make the clones follow orders without question. However, the inhibitor chip was actually used to make the clones follow order 66 which was used to have the Sith bring the long awaited fall of the Jedi Order.
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