In the wanning days of the Sengoku Jidai, two ninja clans, Iga and Kouga, continue to wage a secret war against each other. During the conflict, a Kouga Gennosuke falls in love with Iga Oboro and both hope that their love survives into a time when their two clans finally make peace. However the new Shogun of Japan, Tokugawa Isyasu, perceives a threat and formulates a plan to have the two bitter clans settle their differences once and for all. Gennosuke and Oboro must find a way to stop this battle or risk killing each other.

Shinobi: Heart Under Blade is based on the The Kouga Ninja Scrolls by Futaro Yamada.