Tokumu Houkoukan Yumihari(2004)

Tokumu Houkoukan Yumihari

Following a temporal war that ravaged Japan, the young Shoichi, his two sisters and other children must flee their homeland by boat. During this journey, they are attacked by strange suitor samurai from the future. A girl named Shizue has her face stolen by an unknown life form. The children will be rescued by the crew of a strange battleship, the Yumihari. On board, Shoichi can only note that Shizue's face have completely healed...

(Source: Japanese Publisher, translated)