I believe that it may have been a part of a series. A young boy's father is killed by his science partner who wants to use the technology they built together for evil purposes. The boy's mother is killed trying to save him from an assassination at their gated community where he is hidden in an underground bunker for safety. He is rescued just in time and travels to a forest where they use nanobots to provide natural camouflage to hide them from satellite monitoring. The trees communicate somehow what is going on around them. The nanobots are used extensively in every area of life (i.e. enter bloodstream and heal injuries in the body, create ships for transportation, clothing, tents, etc.) While in hiding with his rescuer, the boy meets several others who have gotten together to hide and live freely. The boy meets a girl there which is the start of a romance.