Summary
- Palpatine's true genius lay in tricking the Jedi into training their own killers, ensuring the success of Order 66 and the downfall of the Jedi Order.
- The Jedi unknowingly primed their clone troopers to turn against them by training them to counter lightsaber-wielding threats, which inadvertently prepared them for the execution of Order 66.
- Palpatine's meticulous planning and preparation over the years resulted in the destruction of the Jedi Order, making him one of the greatest masterminds in the Star Wars galaxy.
In more ways than one, Palpatine manipulated events so that the Jedi themselves trained their own killers in the Star Wars canon. As seen in Star Wars: Episode III – Revenge of the Sith, Palpatine enacted Order 66, a protocol that saw the Grand Army of the Republic turning against their Jedi generals and commanders, brutally ending the Jedi Order which had stood for thousands of years. However, a few key elements leading up to Revenge of the Sith show how Palpatine essentially tricked the Jedi into training the clones to one day overpower them.
Not only was the creation of the clone army for the Republic coopted by Palpatine and Dooku before the Clone Wars had even begun, but Palpatine ensured that the threats the Republic faced would ensure that the troopers would be more than capable of defeating the Jedi generals by the war's end. This was the true sinister genius behind Palpatine's schemes beyond controlling both sides of the conflict. He ensured that the Jedi unknowingly helped orchestrate their own demise.
Your browser does not support the video tag. The Jedi Trained Clones To Take On Lightsaber-Wielders Grievous, Ventress, Savage, Maul… 
Firstly, Palpatine ensured that many of the threats the Jedi and their clone forces would face were dark mirrors of the Jedi themselves. While he wasn't on the front lines for most of the war as leader of the Separatist movement, Count Dooku wielded a red-bladed lightsaber as Palpatine's Sith apprentice, one he used more than once when dueling Jedi such as Anakin Skywalker and Obi-Wan Kenobi throughout the war. However, Dooku did have a handful of agents he sent out on various campaigns who also wielded lightsabers.
Dooku originally had Asajj Ventress, an assassin of the Sith who wielded two red lightsabers during the Clone Warts. There was also General Grievous who led the Separatist armies into battle while collecting and wielding the lightsabers of his fallen Jedi victims. Once Ventress became too powerful, Dooku replaced Ventress with Savage Oppress who also wielded a red lightsaber. Darth Maul also returned during the Clone Wars, claiming the world of Mandalore while wielding both a red lightsaber and the legendary Darksaber.
As a result, there were plenty of opportunities throughout the war in which the clone troopers of the Republic were faced with lightsaber-wielding threats. As such, it stands to reason that the Jedi would have wanted to prepare their soldiers for these types of foes given the high probability that they'd eventually be faced. However, this in turn secretly primed the clones to successfully turn against their generals and commanders with Palpatine's Order 66. The partly helps explain why Palpatine allowed Dooku to have lightsaber and even Force-wielding agents in the first place despite the Sith's Rule of Two (provided they didn't become too powerful as Ventress did).
