Chrono Trigger

From the introduction:

In ancient times, a monster from another world descended from the heavens. Quickly burrowing beneath the planet's surface, it laid dormant within the world's core, consuming its energy. In its slumber, its autonomic systems guided the evolution of the world above it, then harvested the DNA of those species which developed to further its own development. For eons it grew stronger, until at last the day came when it would awaken, and scour all life from the planet.

Its name is Lavos, and in the year 1999, it destroys the world.