The main villain from Call of Duty: Black Ops 2, Raul Menendez, will not be returning in Call of Duty: Black Ops 3, Treyarch has confirmed on their Facebook page.

Treyarch was responding to a user in the comments that asked if he’s returning or whether Menendez’s story ended with Black Ops 2:

So, a few things…
Marshawn Lynch makes a special appearance in the game…he is not “the villain” (i.e. Menendez).
The fictional world of Black Ops 3 carries through from the drone attacks of 2025. For the purpose of the new game, Menendez doesn’t play a part (it would’ve been difficult to do given the multiple endings of BO2).

SOURCE: Treyarch via DumbleWorld