In 2071, roughly fifty years after an accident with a hyperspace gateway made the Earth almost uninhabitable, humanity has colonized most of the rocky planets and moons of the Solar System. Amid a rising crime rate, the Inter Solar System Police (ISSP) set up a legalized contract system, in which registered bounty hunters (also referred to as "Cowboys") chase criminals and bring them in alive in return for a reward. The series' protagonists are bounty hunters working from the spaceship Bebop. The original crew are Spike Spiegel, an exiled former hitman of the criminal Red Dragon Syndicate, and his partner Jet Black, a former ISSP officer. They are later joined by Faye Valentine, an amnesiac con artist; Edward Wong, an eccentric girl skilled in hacking; and Ein, a genetically-engineered Pembroke Welsh Corgi with human-like intelligence. Over the course of the series, the team get involved in disastrous mishaps leaving them out of pocket, while often confronting faces and events from their past. These include Jet's reasons for leaving the ISSP, and Faye's past as a young woman from Earth injured in an accident and cryogenically frozen to save her life.
The main story arc focuses on Spike and his deadly rivalry with Vicious, an enforcer for the Red Dragon Syndicate. Spike and Vicious were once partners and friends, but when Spike began an affair with Vicious's girlfriend Julia and resolved to leave the Syndicate with her, Vicious attempted to have Julia kill Spike. Julia goes into hiding to protect herself and Spike, while Spike fakes his death to escape the Syndicate. In the present, Julia comes out of hiding and reunites with Spike, intending to complete their plan. Vicious, having staged a coup d'état and taken over the Syndicate, sends hitmen after the pair. Julia is killed, leaving Spike alone. His heartbreak feeds his desire to kill Vicious once and for all. Spike leaves the Bebop after saying a final goodbye to Faye and Jet. Upon infiltrating the syndicate, he finds Vicious on the top floor of the building. In a final battle, Vicious is killed and Spike severely wounded. The series ends as Spike descends the main staircase of the building into the rising sun. He falls to the ground, leaving his ultimate fate ambiguous.