The book started with a young guy testing out a Von Neumann machine that he had designed. He was watching a planet from his space ship and the machine went crazy and started replicating until it covered the planet.

He was then enlisted by a mysterious government agent who wanted to use his machine to distract a rogue AI. The agent had a spaceship made of Von Neumann machines that could absorb additional mass and reconfigure itself, even creating a copy of itself at one point to distract an AI.


This sounds like Recursion by Tony Ballantyne. A summary from fantasticfiction.co.uk:

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.

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