Star Wars Order 66: A Republic Commando Novel by Karen Traviss
...Even as the Clone Wars are about to reach an explosive climax, no one knows if victory will favor the Grand Army of the Republic (GAR) or the Separatists. But no matter who wins, the stakes are highest for elite Special Ops clones like the Republic Commandos in Omega and Delta squads–and the notorious renegade Advance Recon Commando troopers known as Null ARCs....
Now... I *really* doubt you're going to read this book unless you've read Traviss's previous three books - for your sake, you'd better, because it won't make sense otherwise. If you do, it's worth it. Traviss hangs a great story on Lucas's hodgepodge of tragedy - and makes the "order 66" make sense within the clone's story. She also continues with her excellent themes of humanizing the clones, and building an interesting background to Mandalorian culture (not to mention happily sprinkling the Mando'a language throughout.)
A tragic story, but well told. I'm sure to buy the paperback to complete my set when it comes out.