The crew of the spaceship Bebop are a partnership of bounty hunters, called "cowboys", who travel the solar system trying to apprehend bounties. Jet Black is the owner of the Bebop, but has partnered with Spike for his diverse combat skills. Though he is reluctant to admit it, Jet has also come to rely on Spike for companionship in the normally solitary field of bounty hunting.
Most episodes revolve around attempts to bring in a specific bounty, but the show also examines the pasts of the main characters and more general past events, which are revealed and brought together as the series progresses. Some of the Bebop's varied targets include small time thugs, gangsters, hackers (known as "net divers" in slang), religious leaders, psychopaths, genetic experiments, mutant creatures and petty thieves.