A reform school for juvenile delinquents established in 200X is actually a government-sponsored laboratory, which makes ultra-human warriors with genetic modification. Three new kids enter the school. Itsuki, who is actually a girl dressed as a boy so she can get into the school to look for her lost brother; Mei, a very quiet, mysterious boy; and Gentaro, an energetic boy who is easily elated by flattery. The three revolt against the school rules and cause the other students to riot. The school turns into a battlefield.

Seventeen years ago, seven subjects of the Japanese government's Siegfried project went missing, calling themselves phantoms and hitting the government with a challenge. The murderer, Mami Kurusu, gets into Kuzu High School, which seems to be phantom-related!

In the summer of 1580, during the Waring States period of Japan, three sole survivors from the massacred ninja schools of Hyuga, Kasumi, and Hagakure come together to defeat Oda Nobunaga and his army of demons using their three mystical blades that have been passed down for generations.