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Mace Windu was the second man in the Jedi council and Yoda was very old. Windu went to Palpatine claiming he was going to arrest him (maybe because he was with two fellow Jedi?), but doubted when he saw Anakin and attempted to kill Palpatine, like: "Heck, an eye witness!".
At this point you might ask yourself: "Why did he go there with 3 Jedi if he wanted to kill Palpatine?" My answer is that the Jedi he took with him were killed in less than 5 seconds. Arguably they were not very good at fighting and were picked for that very reason. "Okay, but why killing Palpatine?" You might ask. Well, if Palpatine would have died, the Republic would need a new leader, and if we are to take Palpatine's reasoning that the Jedi were similar to the Sith in their desire for power, we could reason Windu had certain dreams of ruling the galaxy and the Jedi council.
Killing a dictator would totally give him a lot of support from everywhere, Jedi and politicians alike. He could have announced that the Jedi were going to take temporary control over the Senate to ensure the end of the war and a peaceful transition, so there is little to no doubt that taking Palpatine out of the way would have been tremendously possitive for him, and he knew it.
This can be infered when Windu says to Anakin "if what you told me is true, then you'd earn my entire confidence", like making promises in advance and not wanting Anakin as a witness (I don't think he could suspice Anaking would be capable of turning against him, but rather that Anakin was a very powerful Jedi).
I mean, did he really changed his mind from taking Palpatine as a prisoner to execute him during the fight? His reasoning was that Palpatine had "many contacts"... nothing new or unusual at all that could justify his last minute change of mind.
Finally, it is not only the pink sword (search for it's significance over the internet) or the look he gives Anakin when he sees him, but also the angry face he shows on a scene when fighting Palpatine and the fact that he beheaded Jango in Ep2.
So, what do you guys think? Is there reasonable doubt here? Could the Jedi council be "clouded by the dark side"? I heard the first "side movie" is going to be about Mace Windu, so I guess we might find out the truth in about two years or so...