The clone troopers are not aware of the inhibitor chip or of Order 66, at least not consciously. The chip impacts them at a subconscious level, causing recurring nightmares for the troopers. As Tup draws his last breaths in The Clone Wars, he tells Fives that he is finally free from the mission. When Fives asks what mission he’s referring to, Tup simply says that Fives already knows the mission, the one that manifests itself as a never-ending dream. Fives attempts to uncover the conspiracy, but is taken out before he can. With his last breath, Fives refers to the same nightmares to Rex. Fortunately, Rex and some other troopers are able to eventually remove their chips before Order 66 thanks to Fives’ warning.
