The story is centered around a small group of guerilla freedom fighters on a colonial planet named Deployer, who are known as the "Deployer 7", or "Sun Fang" team. In an unexpected coup, the elected Governor of Deployer becomes dictator and rules Deployer under martial law with the support of Earth's Federation. Fighting for independence from Earth's Federation influence, the freedom fighters begin a rebellion against the Federation's Combat Armors using a Combat Armor of their own: the Dougram.

Demonic Vice-Commander of the Shinsengumi, Toushirou Hijikata, acquires a cursed sword—one which completely rewrites his personality, morphing him from a hard-boiled, no-nonsense cop into a hopeless otaku. As he struggles to break the curse, an ambitious new member of the police force, Itou Kamotarou, seizes the opportunity to depose Hijikata in his bid for power within the organization. However, Itou's scheme is revealed to be more devious than anyone imagined, and the very existence of the Shinsengumi is thrown into peril. In another time and place, the Yorozuya squad is suddenly greeted by a potential new recruit. Before them is a mysterious young woman named Pirako Doromizu who hides a penchant for extreme violence behind her smiling, enthusiastic exterior. However, unbeknownst to Gintoki and the others, Pirako has strong ties to one of the ruling figures of the Kabuki district of Edo, and her arrival sets off a chain reaction that throws the inhabitants of the district into a civil war.

A Corgi can certainly dream! Taking a break from the frequent antics his colleagues get him into, Bebop crewmate Ein envisions himself sipping a tropical beverage on the beachside and scuba diving with Edward amid a barrier reef. In this "picture drama," Ein fantasizes about his ideal summer vacation.

Due to the violence portrayed in the Cowboy Bebop world and violence in Japanese schools, the series was briefly cancelled and an extra session was created as a final episode to the first thirteen episodes aired. Called "Session XX: Mish-Mash Blues," a compilation of clips from previous episodes, it aired on June 26, 1998 on TV Tokyo. The episode was never released on DVD. In it, the characters provide a philosophical commentary and end with the words: This Is Not The End. You Will See The Real "Cowboy Bebop" Someday!