I wonder if we’ll see the aftermath of Order 66, because we know from Rebels that some of the clones rebelled and went into hiding.
The 'Ahsoka' novel touches on this a little bit (apparently the author had access to at least parts of the 'Siege of Mandalore' arc scripts) and in one of the previous panels from a few years back, Dave showed some sketches and shared a few ideas he had of an "Ahsoka on the run" episode. It involved her making friends with giant wolves...because: Filoni.
So I think there's a chance that at least the final episode will be an denouement or epilogue of sorts, taking place after Order 66.
Hell, I wouldn't be surprised if the last shot flashes forwards to Gandalf Ahsoka finishing up her last Clone Wars holocron recording before going to pick up Sabine...
What little is mentioned indicates that Ahsoka and Rex faked each other's deaths to make it look like they killed each other in Order 66, with another clone's body in Rex's armor buried in a shallow grave and her discarded lighsabers to serve as "proof" of their demise.
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