In "Star Wars: Episode III - Revenge of the Sith," Order 66 directs the Clone Troopers to kill the Jedi.
Palpatine secretly activates Order 66 near the end of the Clone Wars, branding the Jedi as traitors to the Galactic Republic. The order instructs clone commanders to turn on their Jedi generals, whom they had fought beside throughout the war. Most clones obey immediately, leading to the galaxy-wide execution known as the Jedi Purge.
The command is part of Palpatine's long plan to destroy the Jedi Order and transform the Republic into the Galactic Empire. Anakin Skywalker, newly renamed Darth Vader, separately leads clone troops in the assault on the Jedi Temple. That distinction can cause confusion: Order 66 triggers the broader massacre of Jedi across the galaxy, while Vader personally commands the Temple attack.
Obi-Wan Kenobi and Yoda survive because they sense the betrayal and evade their troops. The film presents Order 66 as a military command, while later Star Wars canon explains the clones' obedience through implanted inhibitor chips.