Noya Itsuki just transferred to Ebisugawa High School. Since he has always had a fascination with space, he decides to join the Astronomy Club. However, he mistakenly walks into the Asstronomy Club - a club whose members are all female otaku. Itsuki notices that the members are really weird, but he has yet to realize that he joined the wrong club. His life becomes very strange very quickly.

Zoids are beast-like fighting machines used in both everyday use such as transportation, and special use such as war. Some types of Zoids, know as Organoids, are miniature Zoids that are living organisms. These Organoids have the capability to fuse with a non-living Zoid and make it much more powerful. Van (Ban) Freiheit discovers a Zoid Organoid in an abandoned laboratory while running from two strangers piloting Zoids. Also in the laboratory, in an animated suspension tube is a strange girl. He breaks the tube open and takes her and the Organoid with him. Spotting a ruined Shield Liger Zoid outside nearby, the Organoid fuses with it and repairs the damages. Making his escape, Van names the Organoid Zeke, and decides to keep him as a friend. The girl, who says her name is Fiona, wants to find something called Zoids Eve, and so Van, Zeke, and Fiona begin their adventure. (Source: AniDB)

In the previous series "Kite," a killer—Sawa—suddenly disappears after she avenges her parents' death, and no one knows where she is. Several years later, a figure dances airily on the dark side of a big city. She is an angel of death, killing her victim gracefully and disappearing. Monaka is a normal high school student, though this quiet and modest life has a darker side. An angel of death is Monaka's other persona.

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!