Haruta is handsome and smart, Chika is bright and naive. When they were children, they were friends until Haruta's family moved away while he was in the 3rd grade. They meet again during a high school entrance ceremony. After all of these years, Chika is eager to join the wind instrument club. Due to an incident, the wind instrument club is about to be disbanded. Chika can't give up the flute so she attracts Haruta to her side and tries to recruit members from the wind instrument club. The group attempts to solve various cases taking place at their school while they plan to take part in a contest.

During the 16th century, pirates rule the Chinese coastline, pillaging the small villages and terrorizing the citizens. When maverick leader Commander Yu enlists the help of a sharp young general, they devise a plan to defeat the pirates. A violent clash of wit and weapons will decide who will rule the land.

Megumi Noda, or "Nodame" is a piano student at Momogaoka College of Music. An extremely talented pianist who wants to be a preschool teacher, she prefers playing by ear rather than reading the music score. She is messy and disorganized. Shinichi Chiaki is Momogaoka's top student. Born into a musical family, he is talented in piano and violin and has secret ambitions to become a conductor. An arrogant multi-lingual perfectionist who once lived abroad in the music capitals of the world as a young boy, he is trapped in Japan because of his childhood phobia of airplanes and the ocean. They meet by accident and sparks fly!