Above Earth, invisible to humans, float the Heavens—a collection of floating island kingdoms supported by the magic of their godlike inhabitants. The mysterious power source known as Akuto enables this magic to exist, but this is quickly running out. In response to this energy crisis, most of the kingdoms in the Heavens agree to use the minimum amount of Akuto required to sustain themselves, except for the Magical Kingdom. The leader of this kingdom, the Magical King Munto, believes that Akuto can be replenished if he travels to Earth and meets a mysterious girl shown to him by a seer. While Munto sets off on the dangerous journey, the other kingdoms attempt to destroy the Magical Kingdom and acquire the remaining Akuto for themselves. On Earth, Yumemi Hidaka is dealing with her own problems. She can see floating islands in the sky that nobody else can. While her best friend Ichiko Ono believes her, Yumemi wonders if she is going insane. When Munto suddenly appears before her, Yumemi dismisses him as a mere delusion. She is more concerned about her 13-year-old friend Suzume Imamura, who is attempting to elope with her delinquent boyfriend. As the Magical Kingdom nears the point where it will fall from the sky, Munto's quest to save both the Heavens and Earth grows increasingly desperate.

Justy Ueki Tylor is an average 20-year-old man: lazy, greedy, and a passionate womanizer. He plans to land an easy job with the United Planets Space Force that pays decently and is also far away from the rigorous combat raging throughout the galaxy. However, Tylor's dreams of living a simple life are brought to a sudden halt when he stumbles into a dangerous hostage situation. Through one strange mishap after another, Tylor miraculously manages to save the hostages and is awarded command of the decrepit space-cruiser Soyokaze! Now Tylor finds himself in charge of sending mad mercenaries, proud pilots, skeptical colleagues, and harsh commanders through the infinite expanse of the universe, all the while avoiding the looming threat of the Holy Raalgon Empire. What misadventures await the irresponsible Captain Tylor?

Mushi: the most basic forms of life in the world. They exist without any goals or purposes aside from simply being. They are beyond the shackles of the words good and evil. Mushi can exist in countless forms and are capable of mimicking things from the natural world such as plants, diseases, and even phenomena like rainbows. This is, however, just a vague definition of these entities that inhabit the vibrant world of Mushishi, as to even call them a form of life would be an oversimplification. Detailed information on Mushi is scarce because the majority of humans are unaware of their existence. So what are Mushi and why do they exist? This is the question that a Mushishi, Ginko, ponders constantly. Mushishi are those who research Mushi in hopes of understanding their place in the world's hierarchy of life. Ginko chases rumors of occurrences that could be tied to Mushi, all for the sake of finding an answer. It could, after all, lead to the meaning of life itself.

Two years have passed since the end of the Martian Successor Nadesico. Akito and Yurika have disappeared. The Jovians and the Earthlings have joined forces and Ruri is now captain of Nadesico B. As the popularity of Boson Jumping grows, a vast transportation network has been developed. Dubbed the Hisago Plan, this network of Chulip portals holds the answers to the mysteries behind Bose particles and their power. If those secrets should fall into the wrong hands, it could mean big trouble. And big trouble there is. A Martian splinter group has launched an offensive, leaving the United Forces befuddled and desperate. So much so, in fact, that the former crew of the Nadesico is called back to active duty for a special unsanctioned mission-to save us all. Does this menagerie of misfits have what it takes? Who will win the race for the Boson technology? And what the heck happened to Akito and Yurika?