In preparation of the execution of the order, the Jedi Council had been tricked to assign most Jedi to different units of Clone Troopers to assist them in their operations. Order 66 commanded all clone trooper units to immediately attack and kill their Jedi, which at that point were completely unaware of the treachery and highly outnumbered. The Order of the Jedi was almost completely annihilated in just a couple of minutes and thus Order 66 marked the last step to full control of the Republic by Palpatine and the effective birth of the Empire.