It is the year 2100, and on the colonized Moon, a project is under way to explore new aspects of energy. Amami Kurau is the daughter of the chief scientist on the project, and on her 12th birthday, she accompanies her father to the lab to observe the experiments. Then something goes awry, and Kurau is struck by twin bolts of light. In the aftermath, her father is dismayed to find that his daughter is no longer his daughter. Rather, her body is now home to two energy entities with fantastic powers.

Three years since the return of the legendary Space Battleship Yamato, Earth has begun rebuilding itself and has made peace with the Gamilans. However, this recovery comes at the cost of utilizing the forbidden Wave Motion technology. Meanwhile, the notorious former crew members of the Yamato, who have each gone their separate ways, receive a psychic message from the mysterious Goddess Teresa. She urges them to return to their beloved ship and travel to the distant planet Terezart. They are promised a revolutionary power to combat the unprecedented threat of the relentless Gatlantis Empire, who are approaching Earth with all but innocent intentions. Unable to resist her plea, the crew reassembles and sets sail on another perilous intergalactic voyage, one that will test their sheer courage and versatility in the face of an even greater foe.

In the distant future, human beings have been forced to leave earth and migrate to another galaxy. An advanced team of spacecraft arrives at a planet that is to be terraformed. Each member of the team is output by a biological 3D printer.

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.