A few thoughts on the latest version of Malevolence:

On the opening text, is there any reason to specify that six medical stations have been destroyed in the Naboo sector? It would be more straightforward to simply state that “several have recently been destroyed”, since I don’t see the specific number becoming relevant in the episode. Also, to not use the term “destroy” twice in a row, on the previous paragraph perhaps you could change it to - “he has been targeting medical stations, killing thousands of wounded clones”.
That one clone trooper recognizing Ahsoka did feel odd, it could be rationalized that they know her because she’s close to Plo Koon, but still it feels odd that a clone trooper would recognize her this early on in the series, where this is presumably her first proper mission in the Clone Wars.
It also stuck out to me that Plo Koon and Ahsoka quickly move from their fighters to the bridge of the star destroyer, only to move back to the hangar at the end. Though I don’t see a way to avoid that and it’s not really a big deal.

Overall great job once again tightening this set of episodes, this works really well as a continuation of you episode 1, cementing the Anakin/Ahsoka dynamic before moving to other aspects of the series.