Order 66: A Republic Commando Novel

Order 66: A Republic Commando Novel by Karen Traviss
In the final novel of the Clone Wars Republic Commando series, the clone commandos become caught up in Palpatine's scheme to destroy the Jedi, who have been their allies throughout the war. The story overlaps with Episode III: Revenge of the Sith.

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Story continued in Imperial Commando: 501st

This is a prequel era book from the Legends timeline. It may be contradicted by newer books, movies, or TV shows (if so, just think of it as an alternate universe).