Spike and Jet track a bounty head named Giraffe. This leads them to an old man in a wheelchair, and a boy who is not as he appears. The story that began with the Hyper space Gate accident outside Earth then unfolds.
Spike, Faye and Jet are all after Decker, a bounty head in possession of high explosives. They meet V.T, a female space trucker, and team up with her to catch Decker on a dangerous chase through an abandoned mine.
After collecting on a 1.5 million Woolong bounty, Spike gains a fan in Roco Bonnaro. Roco, a small-time gang member, stole a rare and valuable plant from his own gang. Spike finds it's more valuable than he is, but Roco has a different plan for the plant.
Something is carving giant pictures on Earth's surface and the Earth police put out a bounty, drawing in Spike and Jet. A talented computer hacker, Edward, is rumored to be the culprit, but the truth is much different.
Spike, Faye and Jet capture 20 thugs involved in hijacking Astral Gates but none of them was the mastermind with the 12 million woolong bounty on their head. The only clue they have is an e-chess piece that Ed uses to play a game against a cyber opponent over the net: Chessmaster Hex. But are Spike, Faye and Jet just pawns themselves in the chess master's game?
Faye recounts her awakening from cryogenic freezing and a man, Whitney Hagas Matsumoto, who helped her before dying. Jet, however, arrives on the ship having caught him for a bounty. Faye now needs to know what was real.
Jet and his old ISSP partner team up to take on a prisoner transport ship that has been overtaken by the prisoners. One prisoner aboard, Udai Taxim has a history with Jet. Jet finds out how he really lost his arm, and how and why his partner betrayed him so many years before.
Knocked off course by a hit and run, the very hungry members of the out of fuel Bebop find themselves crash landed on Io. Ed and Ein go to look for food and instead come across a mushroom selling drug dealer, Domino Walker. While apprehending him for the bounty, she tests the mushrooms out on the rest of the crew, making for a psychedelic episode.
A mysterious package comes for Faye with a Beta cassette. While Faye runs, thinking it to be from a debt collector, Jet and Spike undertake a arduous search for a player to view it. They find it is a clue to Faye's past.
Jet gets a mysterious note from an old friend, Pao, and finds himself teaming up with his daughter, who uses Feng Shui to decipher it. The two are also chased by syndicate mobsters also searching for him.
Dr. Londes, the leader of the religious cult Scratch, has a large bounty on his head, and Faye joins the cult to get to the bounty. Spike takes to the streets in an effort to get to Dr. Londes while Jet and Ed buy a video game that the cult members use to ascend into the digital being.
Ed places a fake bounty into the system for her own father, in hopes Jet and Spike will lead her to him. They do, and despite a joyous reunion, her absent-minded father immediately abandons her to pursue his work mapping Earth. Ed decides to leave the group, and heads out on her own in search of her father. Ein comes along with her.
Faye briefly teams up with Julia when she assists her escape from a Red Dragon hit squad, and relays a message to Spike about Julia's whereabouts. Spike and Julia finally reunite. The Bebop is severely damaged by the hit squad that follows Faye back to the ship.
Vicious claims leadership of the Red Dragon Syndicate, and Julia and Spike are finally reunited. The two plan to run away as before, but Spike still feels the desire for revenge, leading to a final confrontation with Vicious and the Syndicate.