Jubei Ninpocho: The Wind Ninja Chronicles

All the people of the town of Shimoda have been killed by a plague. The local government, the Togugawa clan, send a team of ninjas to investigate but all but one of them are wiped out by mysterious forces. The only survivor is a woman, Kagero, who is taken prisoner. A samurai mercenary, Jubei, rescues her but his interest in her mission and cause is temporary.