- "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."
- ―Order 66, as defined by the GAR Contingency Orders Initiation
Order 66, also known as Clone Protocol 66, was one of the 150 Contingency Orders of the Grand Army of the Republic which all Clone Troopers were trained to obey by way of a biochip implanted in their brains. The order mandated that the Jedi Order attempted to stage a coup against the Galactic Republic, and all Jedi were to be executed immediately. The biochips implanted within the Clone Troopers activate when Darth Sidious as Chancellor Palpatine sends a message to execute Order 66 to all Clone Commanders when the time has come.
About the time of Stage-3 Embryos, every clone was implanted with an organic, but foreign, tumor. The genetic code in this tumor would program every clone to turn on the Jedi upon activation, but the tumor was incredibly hard to find. Removal of this tumor caused one clone to quickly die afterwards and another to suffer weak spells until he died of separate causes. It was revealed that the Kaminoans knowingly implanted this tumor on new clones in production under the guidance of Dooku and Darth Sidious.