Dooku spills the beans...
... and the Jedi Council fails to investigate Dooku's claims that the Republic was under the control of a Dark Lord of the Sith.
The only reference we get in III regarding Dooku's claims is when Anakin says in response to Mace Windu's, "A Sith Lord?"
"Yes, the one we've been looking for..."
Except if they were actually looking for the Sith Lord in control of the Republic they would have started at the very top--with Chancellor Palpatine, his history, his life on Naboo, who he knows, who he knew, and who he communicated with since the Phantom Menace and the Invasion of Naboo, and beyond.
But they didn't, and the Jedi are caught completely off guard, despite Yoda's claims of the dark side shrouding everything--but funny enough, only on Coruscant--ding ding: Palpatine.