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I've been following the Rebels cartoons quite closely but I can't rule out that I may have missed something. Excluding the trailers (which are really just a collage of snippets from different episodes put together), I don't recall any particular scene where the rebels discover Thrawn to be the identity of their enemy commander.

All I can recall, in chronological order, is that:

  • When Hera first rescued her father on Ryloth, his father merely spoke of the Imperial occupation being taken over by a new commander, in a way that suggests he is unaware the commander is Thrawn. Nobody in the Ghost crew appeared to have any inkling of the same, suggesting they probably do not know about him yet at this point.
  • The first known contact was when Hera encountered Thrawn later while still on Ryloth. She recognised his rank but there's no indication she knows exactly who he is, since he wasn't called by name.
  • Commander Sato appears to have a history with Thrawn. There's no indication if or when he had shared the information.
  • By the time the Rebels started planning a large-scale attack to liberate Lothal, they had already firmly established the enemy commander as Thrawn. This is the first known moment to me when the rebels identified Thrawn by name.

So when did the rebels discover that their main enemy commander is none other than one of the greatest generals in Star Wars history?

  • One of the greatest admirals, you mean. He was not a general. +1 Anyways, I've been wondering this myself – DBPriGuy Feb 2 '17 at 19:20
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I do not have a canon answer and I do not believe there is one.

I would say that Commander Sato revealed Thrawn's identity off screen shortly after their encounter on Ryloth.

However, Rebels are quite aware of the Empire's anti-alien prejudices; furthermore, Thrawn is clearly an alien and of a high rank (possibly the highest in-the-field military rank).

It is not clear whether the Ghost crew was sent to Ryloth as an Rebel Alliance operation or whether it was a "personal" mission. If it was a Rebel Alliance mission, it would probably be standard operating procedure for the leader to report to the chain of Command about the mission. As Hera is the leader and appears to report to Commander Sato, the presence of a new alien of high rank would ensure that Thrawn's presence on Ryloth was reported to Commander Sato.

The fact that Sato and Thrawn seem to have a past makes it likely that a high ranking alien with distinguishable features similar to Thrawn would lead Command Sato to presume that this officer was, in fact, Thrawn and brief the Ghost crew on the Grand Admiral.

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