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Palpatine's Sith identity was a closely guarded secret. Only few people knew that he was Sidious:

Did Grievous know Palpatine was Sidious?

Who exactly knew that Chancellor Palpatine was Darth Sidious?

So, it was surprising to me when I saw Rex addressing Palpatine Lord Sidious (Earlier, no other clone was shown to have known this).

(You can clearly see Rex saying "Yes, Lord Sidious" after receiving Order 66)

How did Rex learn that Palpatine's alter ego name was Sidious? Was the information directly embedded into the brain chip or was there other source?

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There are two theories for this. The first theory is that Rex knew through the brain chip. The second is that Rex knew everything that Maul said to Ashoka and she revealed to him that Anakin would be Sidious's apprentice. Anakin was closest to Palpatine, so Rex might have just connected the dots. It is more likely that it was from the brain chip due to the fact that Cody might have also known Sidious's identity. In Revenge of the Sith he responds to Order 66 with

It will be done my lord.

This implies that he knew that Palpatine was Sidious since he did not respond with "yes sir" "or yes Chancellor" but rather my lord. Hope that helps. (My source is Revenge of the Sith and the video below)

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