In the year 2063, space travel is feasible and commercially available. As the cheerful Aries Spring arrives at the spaceport to attend a camp on the distant planet McPa, her purse is suddenly snatched by a reckless thief. Luckily, the athletic Kanata Hoshijima is able to retrieve it for her, and Aries soon discovers that he is among the group of teenagers who will be traveling with her on the excursion as team B-5. Upon arriving at their campsite, the group's trip takes a turn for the worse when a strange sphere of black light sucks them into the vast reaches of outer space. Stranded with seemingly no hope, they find an abandoned ship nearby that provides them with the means to return home. However, they soon discover that they are not as close to their campsite as they initially thought, but are in fact thousands of light-years away from home. With this realization, the nine members must cautiously manage their resources, maintain their strength, and unite as one to conquer the darkness of space together. While the reason behind their trip's sudden obstruction remains unknown, they nevertheless embark on the treacherous voyage back home aboard their new ship, the Astra.

Crime is timeless. By the year 2071, humanity has expanded across the galaxy, filling the surface of other planets with settlements like those on Earth. These new societies are plagued by murder, drug use, and theft, and intergalactic outlaws are hunted by a growing number of tough bounty hunters. Spike Spiegel and Jet Black pursue criminals throughout space to make a humble living. Beneath his goofy and aloof demeanor, Spike is haunted by the weight of his violent past. Meanwhile, Jet manages his own troubled memories while taking care of Spike and the Bebop, their ship. The duo is joined by the beautiful con artist Faye Valentine, odd child Edward Wong Hau Pepelu Tivrusky IV, and Ein, a bioengineered Welsh Corgi. While developing bonds and working to catch a colorful cast of criminals, the Bebop crew's lives are disrupted by a menace from Spike's past. As a rival's maniacal plot continues to unravel, Spike must choose between life with his newfound family or revenge for his old wounds.

All his life, Shiki has been surrounded by machines. At Granbell Kingdom, a long-abandoned amusement park, he is the only one of his kind around. That is, until Rebecca Bluegarden and her feline companion Happy arrive, unaware that they are Granbell's first visitors in one hundred years. Their goal is to make fun videos for their B-Cube channel, but what they find instead is a friend in the socially awkward Shiki. When Granbell becomes too dangerous for the three of them, they set off on an adventure through the Sakura Cosmos. They hope to make more interesting videos and even find the elusive goddess Mother, while Shiki wants to make more friends, spurred on by the words of his late grandfather. Of course, the journey will not be easy, as no one has seen Mother before, but Shiki is determined to reach his goal and explore the boundless reaches of space together with his new friends.

Now in possession of the Edens Zero, Shiki Granbell has gathered the Four Shining Stars. With the help of his new friends, Shiki will be able to breach Dragonfall—the border of the Sakura Cosmos swarming with mechanical dragons. Once that is achieved, he can continue his quest to find the goddess Mother. Before the Edens Zero crew can advance their journey, they notice a mysterious warship following them. Upon learning that the ship—the Belial Gore—belongs to Drakken Joe, Shiki and his crew attempt to infiltrate it, intent on figuring out why the Dark Alchemist is after them. In the process, the Edens Zero is taken hostage by Drakken's subordinates. Though they are in a tight situation, Shiki refuses to back down. Working together with his friends, Shiki will have to take down the Dark Alchemist if he hopes to make it out of the Belial Gore alive.