Final Fantasy Legend III

A creature known as the Pureland Water Entity engulfed the world in a great flood. The entity drew monsters onto the land and low lying cities have been abandoned. As a party of four warriors sets out to confront the entity, several youths from the future arrive to help, and it is realized that the Entity's destruction is occurring in the past and future as well. The group then collects pieces of the ship Talon in the past, present, and future to defeat the Entity.