The following contains spoilers from Yoda #3, on sale now from Marvel Comics.
Star Wars fans know that the Sith made multiple attempts at destroying the Jedi Order. Over the millennia, there were various wars and large-scale conflicts, but the Sith made one of their biggest moves during the Old Republic when Darth Malgus sacked the Jedi Temple on Coruscant. There's an off-handed chance that that event could be shown in The Mandalorian Season 3, but that still wouldn't live up to the horrors of Order 66.
Darth Sidious' sinister plan was activated with a single command, and it ended with the annihilation of thousands of Jedi. However, as simple as his plan seemed, it was multi-faceted, and it took years of preparation. The thing is, Yoda knew how Sidious' plan started. In fact, Yoda #3 (by Cavan Scott, Nico Leon, Dono Sánchez-Almara, and VC's Joe Caragagna) showed how Yoda learned a lesson that should have warned him about Order 66.
Yoda's Unofficial Padawan Didn't Portray The Right Image
The first two issues of the Yoda comic showed Yoda abandoning the Jedi Order and traveling to the distant world of Turrak to help defend the Scalvi from Crulkon pirates. He stayed with them for a long time, and some Jedi thought that he was becoming too attached. However, he eventually left because a young Scalvi -- an apprentice of sorts, named Bree -- killed one of the Crulkon in cold blood. Yoda #3 picked up years later when Bree was an adult. He finally understood that his violent actions were wrong and regretted killing the Crulkon. But he hadn't properly educated his niece and nephew.
They thought that he was a war hero, who helped liberate the Scalvi from the Crulkon pirates and even acted out the scene. That nearly got them in trouble because the Crulkon attacked after years away, and the niece and nephew wanted to help. So, they kidnapped the Crulkon leader's daughter. Luckily, Yoda came back, and Bree was able to broker peace. Yet, there was an important lesson tucked in the story. Bree didn't project the right image to his people, and it nearly ended in disaster. The point was simple. If Bree wanted to advocate for peace and non-violence, then he should have denounced his violent actions much earlier. Unfortunately, Yoda saw all that happen, and he fell into the same trap during the Clone Wars.
Yoda Should Have Considered the Implications of the Jedi's Actions
Over the years, the Jedi had fought in various wars, but their image had remained sound. They were peacekeepers, and the public knew that. Their attire even identified them as Jedi, so everyone knew who and what they stood for. That's why the Clone Wars signaled such a big turning point. The Jedi that once served as peacekeepers started to actively lead the armies of the Republic. That was one of the first steps in Order 66. In order for the Jedi to be framed as traitors, they needed to be portrayed as self-serving soldiers, not selfless peacekeepers.
So, Palpatine used his power to push them into the war effort. Because of what he saw with Bree, Yoda should have known that something was wrong with being pushed into a war - but he didn't stop it. Of course, the Jedi master wanted to serve and protect the galaxy, but he still should have considered the optics. Being at the forefront of the Republic's war was bad for the Jedi Order's image. And if Yoda hadn't blindly joined in the Clone Wars, it would have been much harder for Palpatine to execute Order 66.