After Order 66, the Galactic Empire was formed and the order remained in act during the Galactic Empire era. It means that the Jedi are traitors and gives orders for Clones to kill their Jedi commanders.
Order 66 is an order in the Galactic Republic's army for Clone Troopers. Order 66: In the event of Jedi officers acting against the interests of the Republic, and after receiving specific orders verified as coming directly from the Supreme Commander (Chancellor), GAR commanders will remove those officers by lethal force, and command of the GAR will revert to the Supreme Commander (Chancellor) until a new command structure is established.
