Order 66 was the most infamous command given in Star Wars history, signaling the end of the Galactic Republic and beginning the near collapse of the Jedi Order. While Clone troopers were forced to obey Order 66 due to the biochips implanted in them in canon, the Karen Traviss' Legends series Republic Commando paints a far darker portrait of its execution.
The Republic Commando series depicts Order 66 as a command all Clone troopers were taught, rather than one they were forced to obey. At first glance, the Order seemed perfectly reasonable, as it was originally created by Sifo-Dyas as a way to put down rogue Jedi who went against the Republic. This order was also above Order 65, which was intended to put down the Supreme Chancellor if a similar issue arose.
In Republic Commando: True Colors, Order 66 is described as such: "In the event of Jedi officers acting against the interests of the Republic, and after receiving specific orders verified as coming directly from the Supreme Commander (Chancellor), GAR commanders will remove those officers by lethal force, and command of the GAR will revert to the Supreme Commander (Chancellor) until a new command structure is established."
Traviss depicts the brutal reality of the Clone Wars, which created a lot of tension between Clone troopers and their Jedi commanders. Essentially bred as soldier-slaves for the Republic, the life of a Clone trooper was basically equivalent to that of a droid. Their sped-up aging process ensured that Clone troopers would never reach a fulfilling life beyond battle, even though Clones were biologically identical to humans and capable of biological reproduction. Clones were also capable of a full-range of human emotions, which created inner turmoil regarding their brief existence.
Many Clone troopers also grew tired as the war dragged, as they were forced to watch their brethren fall in battle. Republic Commando: Order 66 details Delta Squad Commando Scorch's inner frustrations toward this loss of life, as he hears the names of thousands of fallen Clone troopers. "Scorch couldn't now name half the squads in his batch at the Tipoca training center, let alone the men in them. He felt ashamed, as if he'd betrayed them," the passage reads. As the war dragged on, many Clone troopers began to resent the Jedi for these casualties, even calling their competence into question.
The Jedi's attitudes towards Clone troopers weren't any better, as they merely saw them as disposable. They were especially indifferent to Clone commandos, who they viewed as state-sanctioned bounty hunters for the Republic. Despite their indifference toward these squads, the Jedi understood their necessity in the war. "That's the problem with having intelligent clones trained by a ragbag of undisciplined thugs — they've turned out at best idiosyncratic, at worst disobedient. But they'll probably win the war for us. Tolerate them," Jedi Master and Director of Special Forces General Arligan Zey explained in Republic Commando: Triple Zero.
As a result of this shared dissatisfaction, it wasn't difficult for many Clone troopers to turn their guns on their former commanders, but a few notable outliers remained. Ion Team, which was led by Captain Climber, not only disobeyed the order, they turned their guns against the forces of Commander Salvo who attempted to ambush a group of Jedi. Other Clone squadrons, such as Omega Squad, Delta Squad and Ordo Skirata, disobeyed the order as well, but feigned compliance to avoid suspicion from the Empire. While Clones in those latter squadrons held tenuous relationships with the Jedi, they were far more skeptical of Palpatine who unveiled new Centax clones that aged normally.
While canon strips the Clones of their culpability in Order 66's execution, Legends confronts their betrayal head on. This nuanced depiction of Order 66 is darker than canon, but Republic Commando provides depth to its execution by humanizing its Clone perpetrators and their suffering.