On Dathomir, the clan of the Nightsisters begins their ritual.
On a vessel rocketing through lightspeed, Darth Plagueis begins his.
Master Yoda is perhaps the most powerful of the Jedi Order, if you don't count Kina, and no one really does. That doesn't mean his mind can't be controlled, but it means they can't use the normal methods, even those that are theoretically capable of controlling Jedi. They have to be a little more cautious.
When he sent his instructions, Palpatine had considered trying to force Yoda to turn on his allies. Kill Windu, kill Kina, kill the rest of the Order, and get Palpatine to safety. The trouble was, though, that just wasn't something Yoda would do. If the thought entered his head, he would recognize it as alien, and then he would be on guard. Everything would break. There are plenty of people in the galaxy weak enough to fall for that, but Yoda isn't exactly the type to let someone else's ideas influence his head.
His own ideas, though...
Plagueis and the Nightsisters can't force Yoda to be someone other than Yoda. What they can do, though, is be selective over which parts of Yoda are more active. There's a part of Yoda that knows they have to present a public face of protectors who would never kill anyone innocent, who knows that they still don't have complete, undeniable proof, and it's saying to keep Palpatine alive. There's another part of Yoda that knows Palpatine is dangerous, who knows that leaving him alive will be too dangerous and give him opportunities to escape, who knows that Palpatine might have plans in motion that account for his unconsciousness. Normally, it would be a tough decision.
Today, Yoda is sure of himself. One part of him just happens to be a little louder than the other, that's all. Nothing out of the ordinary.
And so he shakes his head, and he puts both lightsabers into his pockets.