Autonomous features a rakish female pharmaceutical pirate named Jack who traverses the world in her own submarine. A notorious anti-patent scientist who has styled herself as a Robin Hood heroine fighting to bring cheap drugs to the poor, Jack's latest drug is leaving a trail of lethal overdoses across what used to be North America--a drug that compels people to become addicted to their work. On Jack's trail are an unlikely pair: an emotionally shut-down military agent and his partner, Paladin, a young military robot, who fall in love against all expectations. Autonomous alternates between the activities of Jack and her co-conspirators, and Elias and Paladin, as they all race to stop a bizarre drug epidemic that is tearing apart lives, causing trains to crash, and flooding New York City.