The last few episodes of Person of Interest have shown that the Stanton virus is behind the Machine's recent glitchy behavior. But EP Greg Plageman gave spoilers to TV Guide that suggest the Machine is going to start fighting back:
"What's really interesting about the Machine is whether or not you believe it is an evolving organism. What happens when an organism like that comes under attack? The question to ask is: Have we seen all the facets of the Machine and its true power?"
What do you think the Machine will do to protect itself?