Order 66 was a clone protocol that ordered all Clone Troopers to execute/attacked all the Jedi which branded the Jedi as traitors. They were trained to obey with out hesitation or question. and called for their immediate execution without question or hesitation. The issuing of the order by Supreme Chancellor Palpatine marked the formal beginning of the extermination of the Jedi Order, and the rise of the Galactic Empire leaving few survivors.
Clone Protocol 66 was a inhaler bio-chip implanted in all Clone Troopers that would make them attack the Jedi.