Cowboy Bebop: The Movie is set on Mars in 2071, 49 years after Earth was mostly abandoned after a catastrophe. Humanity has settled on other planets and moons in the solar system. The film’s protagonists are legalized bounty hunters who travel together on the spaceship Bebop. They are Spike Spiegel, a former associate of the Red Dragon crime syndicate; Jet Black, a former police officer and owner of the Bebop; Faye Valentine, a woman who was once a fugitive from bounty hunters; Edward Wong Hau Pepelu Tivrusky IV (Ed for short), a girl with genius computer skills; and Ein, an artificially enhanced ”data dog” with human-level intelligence.
Days before Halloween, a man explodes a truck in Mars’ capital city, spreading what is assumed to be a new pathogen that kills or sickens over three hundred people. In response, the Mars government issues a record bounty of 300 million woolong for the culprit’s capture. Faye, who was pursuing Lee Sampson, a hacker that was apparently driving the truck, sees the terrorist and the Bebop crew decide to take on the bounty. Each follows different lines of inquiry. Ed, using a tattoo on the attacker’s wrist, manages to identify him as Vincent Volaju, a former member of a military squad apparently killed in the Titan War. In reality, Vincent was the only survivor of a test involving the pathogen, having been immunized with a test vaccine: made an amnesic, he suffers from hallucinations, and his inability to tell dreams from reality eventually drove him insane.
Jet learns that the truck was the property of Cherious Medical Pharmaceutical Company, who illegally manufactured the pathogen as a biological weapon. Looking for information on the pathogen, Spike is given a sample by a man named Rashid, who was the former lead on its development. Spike also encounters Elektra Ovirowa, an agent of Cherious Medical. Upon examination, the ”pathogen” proves to be a type of protein-based nanomachine that mimics human lymphocytes then breaks down into protein after death, making it undetectable. Attempting to infiltrate Cherious Medical, Spike fights with Elektra, planting a listening device on her. Elektra, who is sent by Cherious Medical to kill Vincent, is tailed by Spike, who attempts to take down Vincent on a train. Vincent easily defeats Spike, severely wounding him and throwing him from the train before releasing another cloud of the nanomachines: everyone in the train dies except Elektra, who was unknowingly immunized when she had been in a relationship with Vincent prior to the test on Titan. She secretly gives a friend in the company a sample of her blood to prepare a stock of vaccine. During this time, Faye relocates Sampson, who has been working with Vincent, but fails to catch him. Ein and Ed manage to find him again, but the two run off before Faye can get there. She arrives just as Vincent breaks one of the nanomachine containers with him, killing Sampson. Although Faye is also infected, Vincent gives her some of his blood through a kiss, immunizing her.
After Spike recovers and has a final talk with Rashid, he and Elektra are captured by Cherious Medical, who want to suppress all knowledge of the nanomachines’ existence. The two escape from Cherious Medical, grabbing the newly produced vaccine on the way. In turn, Faye escapes after Vincent goes to trigger an attack on the city that will eventually kill everyone on Mars. After the group reunites, it is determined that Vincent will spread the nanomachines by exploding the giant jack-o’-lantern balloons used in the Halloween parade: Jet has a troop of old aircraft spread the antibodies over the city while Faye heads for the weather control center and causes it to rain on the city, aiding the spread of the vaccine. Spike and Elektra separately head to confront Vincent. Spike arrives first and the two battle to a standstill, then the nanomachines are released and Spike is temporarily weakened by them. As Vincent prepares to kill him, Elektra arrives and shoots Vincent. Having wanted to die since Titan, Vincent does not defend himself and thanks Elektra for their time together before dying.