During the final lightsaber duel between Yoda and Sidious, it is revealed that Count Dooku was actually sent undercover to infiltrate the Sith by Master Windu and Yoda. Qui-Gon was aware of this plan as well, a secret which he took with him to the grave.

Palpatine merely replies, "Yes, I know," cackling triumphantly.

This is the pivotal "betrayal" Anakin learns about the Jedi, for the entire goal was to topple the corrupted Republic, which the Jedi had been aware for ten year, had been under the influence of the Sith. Obi-Wan was not told of this plan, and has no argument when Anakin explains this to him before he falls into the lava. In fact, Obi-Wan is sympathetic to Anakin, and tries to save his life, but Anakin lets go of Obi-Wan's hand, plummetting into the molten chasm below.