Star Wars: Order 66: A Republic Commando Novel (Tom Thorne Novels)

The fourth novel in the Republic Commando series, where multiple storylines come to a head in the wake of Emperor Palpatine's issuing of the notorious Order 66.
When the order comes through, the clone troopers of Delta and Omega squads must decide whether to turn on their Jedi generals - or to disregard the command and face dire consequences.