Recursion — Tony Ballantyne

It is the twenty-third century. Herb, a young entrepreneur, returns to the isolated planet on which he has illegally been trying to build a city -- and finds it destroyed by a swarming nightmare of self-replicating machinery. Worse, the all-seeing Environment Agency has been watching him the entire time. His punishment? A nearly hopeless battle in the farthest reaches of the universe against enemy machines twice as fast, and twice as deadly, as his own -- in the company of a disarmingly confident AI who may not be exactly what he claims...

Little does Herb know that this war of machines was set in motion nearly two hundred years ago -- by mankind itself. For it was then that a not-quite-chance encounter brought a confused young girl and a nearly omnipotent AI together in one fateful moment that may have changed the course of humanity forever.