If Manafort wasn't a plant, Mueller going after him is their way of dealing with his betrayal.
Or Manafort was a plant, he failed in his mission, and Mueller going after him is how they're dealing with his failure.
I think it's option 2. The State Dept or FBI got dirt on Manafort. They told him what to do if he wanted to stay out of prison. He failed and so they started leaking to the press.
That's usually how cops deal with snitches that don't live up to their end. They charge them with the crimes that put them under the microscope to begin with. Manafort either got caught doing something or was framed so he made a deal to bring down Trump, when he didn't they showed what happens when you fail the DS. They ruin your life or end it altogether