The plot might involve a clone who has a unique experience that makes him realize the wrongness of Order 66. For example, he could have been saved by a Jedi in the past. This clone then convinces other clones around him to disobey. They might join forces with some remaining Jedi and form a resistance against the new regime that's trying to take over after the purge of the Jedi. It could be a story full of action, as they fight against the forces that still support the execution of Order 66.