I don't think the machine has a master anymore. Was that not the end game of the episode? The machine also gave the government group a new number. I think it is now basically doing what it wants now. The machine definitely has a plan for Root, the question is what is that plan.
I wonder if they'll go down the road where the machine could become some sort of threat, and use Root and/or the government group to do something crazy that Finch & Reese will have to stop. Since the machine is basically alive now, there is no telling what it is capable of, or what it grows/evolves into.