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In the beginning of Episode II, Padmé and Palpatine meet and have a little argument, and Palpatine seems to guess what Padmé is going to say:

Padmé: Chancellor, if I may comment, I do not believe...

Palpatine: ...that the situation is that serious? (pause) Oh, but I do, Senator.

Padmé doesn't confirm that Palpatine "guessed" right and Palpatine seems absolutely sure that he knew what she was going to say - obviously, since a Sith lord is certainly capable of doing that. Yoda gives Palpatine a glare, which I interpret as 'suspecting'.

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Did Yoda suspect Palpatine already at this stage being a Sith lord or even a force-sensitive human? If he did, why didn't he discuss it with Obi-Wan or Mace or anyone? If he didn't, why the glare?

  • During that conversation, Yoda seems to be mostly pre-occupied with the idea that Dooku is turning out to be an enemy of the Republic. It's not until later that they even start to imagine that he's turned to the dark side of the Force. – Valorum Mar 30 '16 at 20:34
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According to the film's official novelisation, Mace Windu and Master Yoda have been discussing the possibility of someone close to the Chancellor being a Sith Lord, in line with Dooku's admission in the previous film.

With what could only be described as a truly stunning lack of judgement, they ruled Palpatine out of consideration almost immediately, reasoning that he's too powerful to be a truly bad guy or he'd have already done something bad.

There's no indication that at the earlier meeting (in AotC) that they had any serious suspicions that Palpatine was a dark Force user or that he was anything other than a power-hungry politician par excellence.

“But he doesn’t have the authority to interfere with a Jedi investigation …” Obi-Wan frowned, suddenly uncertain. “Does he?”

“The Senate has surrendered so much power, it’s hard to say where his authority stops.”

“It’s that bad?”

Mace’s jaw locked. “The only reason Palpatine’s not a suspect is because he already rules the galaxy.”

“But we are closer than we have ever been to rooting out the Sith,” Obi-Wan said slowly. “That can only be good news. I would think that Anakin’s friendship with Palpatine could be of use to us in this-he has the kind of access to Palpatine that other Jedi might only dream of. Their friendship is an asset, not a danger.”

“You can’t tell him.” “I beg your pardon?”

“Of the whole Council, only Yoda and myself know how deep this actually goes. And now you. I have decided to share this with you because you are in the best situation to watch Anakin. Watch him. Nothing more.”

“We-” Obi-Wan shook his head helplessly. “We don’t keep secrets from each other.”

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