Might & Magic VI-VIII: A world once part of a galactic community has been cut off due to a millennia long interstellar war. Because of this, the world's culture and technology has fallen back into medieval times, and the majority of bioengineered creatures have disappeared or gone rogue. Oh, and magic exists.
I did have an idea just a couple of weeks ago about a superhero game set in ancient times, except for the magic being nanotech, the gods being supercomputers, and the whole thing actually being thousands of years in the future of our earth, post-peaceful-end-of-civilization.
And, I'm not naming it, but an adult webcomic I saw once had a high concept that ancient Atlantis had discovered the secrets of how to use magic before it was destroyed.
When its ruins were rediscovered, worldwide culture underwent a revolution in order to facilitate the physical and emotional rituals required to harness magic.
So yeah, I'm sort of suggesting, you could have something like dormant nanotechnological microbes reactivate, or an ancient magic-suppressing curse on the world expire, or an intersection with some parallel dimension, or something else with the general idea that something disappeared millennia ago has come around again.
One more: In Golden Sun, alchemy and psynergy used to be common on Weyard, but was sealed away to prevent a great war (I think).
When Mount Aleph erupts, psynergy crystals are scattered throughout the world, granting powers to anyone exposed to them, but also turning many animals into monsters.