The latest Star Wars tie-in, an anthology for Star Wars: The Clone Wars, reveals the Force warned Master Yoda about the Clones' impending betrayal. The Clone Wars were the perfect Jedi Trap, engineered by Palpatine so the Jedi would lose the minute they begin to fight. They left the Jedi overextended, grief-stricken, demoralized and compromised, and as a result unable to sense the warnings of the Force. The tragic tale of the Clone Wars is told in the popular animated series that recently concluded on Disney+.
And, of course, they culminated in Order 66. When Palpatine judged the time right, he issued a command that robbed the Clone Troopers of their free will and forced them to turn on their Jedi Generals. The Jedi received no warning, because their killers had no animosity, no anger and no hatred, just a desire to obey orders. Jedi died all over the galaxy, with only a handful surviving, notably including Obi-Wan Kenobi and Master Yoda.
Lucasfilm has recently published an anthology book, Stories of Light and Dark, that allows popular authors an opportunity to reinterpret key episodes of Star Wars: The Clone Wars. One of the most striking, by Jason Fry, is an adaptation of the season 1 episode "Ambush." In this episode, Master Yoda found himself caught up in an adventure on the planet Rugosa, operating alongside three Clone Troopers. It was already a strong episode, but Fry's story adds more depth to it, revealing Yoda received a vision from the Force - one that clearly warned him about Order 66.
Yoda found the clones disturbing, not least because he noticed they were treated more like mindless droids than people; because they were mass-produced they tended to be thrown at targets without much interest in their survival, and they were not encouraged to acknowledge their individuality. "Made for war these children were," Yoda reflected. "Made by the millions. Disposable their makers consider them." But worst of all, as far as Yoda was concerned, was a fundamental flaw in the clones' character; an instinct for obedience that he sensed had practically been programmed into them. As he meditated upon this, the Force granted him a vision of "another presence - one that felt like a vast storm in the Force, full of malice and greed." The Jedi Master intuited this storm was a vision of the future, granted by the Force, one somehow associated with the Clone Army.
But Master Yoda made the wrong decision. He had seen thousands, perhaps tens of thousands, of Padawans become distracted by glimpses of the future. His distrust of ancient Jedi prophesies seemed to have been proved right when Count Dooku left the Jedi and became a Sith Lord, because Dooku was one of the few Jedi who had studied the ancient Jedi prophesies, and he seemed to prove they would lead you down a dark path. Thus, while Yoda allowed the Force to guide him as it wished, he did not believe in pursuing visions - nor even in exerting effort in order to understand those granted by the Force. All would be revealed in time, he figured.
All was indeed revealed in time - but too late. Had Master Yoda only joined those dots, had he only sought the Force and attempted to divine the warning he had received, he would have begun to uncover the horrific secret that lay at the heart of the Clone Wars. But he did not, and the galaxy's fate was sealed.