The story follows Benio "Haikara-san" Hanamura, who lost her mother when she was very young and has been raised by her father, a high-ranking official in the Japanese army. As a result, she has grown into a tomboy - contrary to traditional Japanese notions of femininity, she studies kendo, drinks sake, dresses in often outlandish-looking Western fashions instead of the traditional kimono, and is not as interested in housework as she is in literature. She also rejects the idea of arranged marriages and believes in a woman's right to a career and to marry for love.
Takamachi Nanoha is a normal third-grader who feels a little useless and out-of-place with no purpose. Then one day, she saves a ferret, who turns out to be a mage from another planet who came to this planet to search for the jewel seeds. Nanoha agrees to help, but this task gets complicated when another girl arrives to steal them.
It's the 22nd century and Shambhala city reporter Youko and her android boyfriend, bodyguard and cameraman Pete are hunting the enigmatic criminal Mr. X. Their search leads them to the Rainbow Tower, were Youko is taken hostage and Vito must battle to save her by destroying the program of the Tower's central computer to prevent X's escape.