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After ROTS when Dooku, Grievous, and the Trade Federation frontrunners were all killed and the CIS was defeated, what happened to the millions of droids scattered across the galaxy? Was this ever touched on?

Vader deactivated them after he killed the separatist leaders on Mustafar.
Later, some battle droids appeared in a Rebels episode and in the Vader comics.

I know they were deactivated, but what happened to the droids themselves?

Left to rot in some places, scavenged by others for parts or security, melted down, ect. Anything really.