Most episodes are named after a musical concept of some sort, usually either a broad genre (e.g. "Gateway Shuffle") or a specific song (e.g. "Honky Tonk Women" and "Bohemian Rhapsody").

[2] In its original run on Adult Swim, episodes 6, 8, and 22 were initially skipped due to their violent and destructive themes in wake of the September 11 attacks.

The main characters include Spike Spiegel, a laid-back former member of the Red Dragon Syndicate (a criminal organization) and hotshot ace pilot; Jet Black, a retired cop and the owner of the Bebop; Faye Valentine, a gambling-addicted amnesiac who always finds herself in financial debts; Edward Wong Hau Pepelu Tivruski IV (nicknamed "Ed"), an eccentric computer hacking prodigy from Earth; and Ein, a "data dog" as the group's pet.

Jet meets an old contact at the ISSP and only learns that the police force aren't interested in investigating due to petty corruption but the tanker explosion was traced back to Cherious Medical, a pharmaceutical company who never reported the truck missing.

With Faye's lackluster help, Edward and Ein identify the driver who survived the tanker explosion as Vincent Volaju, a soldier who is listed as deceased.

After some computer hacking by Ed, they find out the supposed pharmaceutical company was a cover for building protein nanobots, which were mimicking the lymphocytes, and were meant to be the ultimate weapon.

While looking for the man who sold him the vase, Spike finds out the organic microscopic robots were tested on soldiers but so was a vaccine, which was only injected into Vincent who went AWOL and insane.