Final Fantasy Legend III

Millennia ago, a fierce battle was waged for control of an idyllic world known as Pureland. After much fighting, the brave warriors of Pureland were protectively sealed in their own dimension, away from the rest of the universe. This was done by means of Talon, a powerful space craft capable of traveling through both time and space. Centuries have passed and the would-be master of Pureland have managed to create a rift in the galaxy, sending the Pureland Water Entity to devour all that stands in its path. You must journey through past, present, and future to find the 13 pieces of the now-divided Talon. Only then can you save the universe from total destruction.

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.