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?

In an alternate 21st century, the robotics industry undergoes a period of rapid advancement worldwide. By the year 2050, Japan has firmly established itself as the leader in robotic technology and manufacture with Daiwa Heavy Industries. As the technology evolves to include robotic enhancements to the human body, the blurring of the line between man and machine triggers a sudden shift in world opinion. In response, the U.N. passes a unilateral ban of further research and development on robotics in 2067. Japan fiercely objects to this ban, but is unable to prevent its passage. In protest, Japan withdrew from international politics and chose to pursue a policy of high-tech national isolation. While only trade continues, Japan disappears from the world scene. Ten years later, a series of bizarre incidents lead the American technology police agency SWORD to believe that Japan has concealed extensive development of banned technologies through the use of the RACE network. SWORD dispatches a unit of special agents to infiltrate Japan and gather intelligence on the country. Vexille, a veteran agent among the group, uncovers the horrifying truth behind the ten years of isolation.

Since ancient times, shrine maidens who wield swords have been exorcising "aratama," strange existences that threaten the human world. These young women who wear school uniforms and a sword are called "Toji," and they serve as an official unit within the police force as a "special religious service police squad." The government authorizes the Toji to wear swords and serve as government officials, and the government has set up five schools throughout the country for the girls to attend. In the spring, the five schools send their best Toji to compete in a tournament. As the tournament comes closer, all of the representatives rigorously train themselves in order to get stronger and improve their skills.

From the heavenly object known as the Chaos Pearl, two elements are extracted: the Spirit Pearl and the Demon Orb. In an attempt to suppress their power, the Lord of Heaven sends the Spirit Pearl to Earth to reincarnate as Ne Zha, the third son of Li Jing, while the Demon Orb is scheduled to be destroyed by a lightning strike. However, because of a conspiracy by the Dragon King to steal the Spirit Pearl for his own son, Ne Zha is instead reincarnated with the Demon Orb. With no way to remove the cursed effects of the Demon Orb, Ne Zha is raised under the belief that he will become the great demon hunter the Spirit Pearl destined for him to be. Fighting against his chaotic and mischievous nature, Ne Zha must decide whether to accept his evil fate or rebel against it to prove he is worthy of the future his parents foretold.