Summary
- Order 66 was not a one-time event, but an ongoing law enforced by the Empire. The Inquisitors played a vital role in its final stage.
- The Inquisitors, being Force-sensitive themselves, were seen as a threat by Vader and the Emperor. They had to be eliminated to ensure the complete extinction of the Jedi.
- The deaths of all the Inquisitors would have marked the end of Order 66. Their power struggles with each other made it necessary for Vader to wipe them out.
The execution of Order 66 is easily one of Star Wars' greatest tragedies, but it has a much more massive scale than some might think, as revealed by Darth Vader and his Inquisitors. The Inquisitors, who first appeared in the animated Star Wars Rebels series, were a vital part of enforcing Order 66 long after the first command was given by Emperor Palpatine to the clones. With Darth Vader placed in charge of these Force-sensitive hunters, they were all held to high standards, and thus succeeded very well in continuing the extinction of the Jedi Order.
Despite working so closely with them, it's been well-known that Vader was never fond of the Inquisitors. Much of this has to do with the Sith Rule of Two, as Vader no doubt feared being replaced by another Force-sensitive dark side wielder, but there were other forces at work. Vader often pitted the Inquisitors against one another as a result of his disdain for them, but most importantly, he rid the galaxy of their influence by the time of the Galactic Civil War. As it turns out, Vader's actions were tied more closely to Order 66 than they were to his hatred of the Inquisitors.
Your browser does not support the video tag. Order 66 Remained In Legal Force Throughout The Empire 
Order 66 was made into law by Emperor Palpatine, rather than being just a one-time event ordered at the end of the Clone Wars. This means that anything associated with the Jedi or the Force were in violation of not just the original Order 66, but the law that was actively being enforced by the Empire. While Inquisitors were the ones who dealt directly with Force-sensitive threats and Jedi, stormtroopers themselves could still arrest and apprehend people on suspicion of them trying to maintain some kind of connection to the Force. Since Order 66 wasn't a one-time event, then, it had multiple stages – and the Inquisitors were a vital part of its final stage.
