This is the story of the game BioShock, with its own Equestrian twist.
Years into the reign of Princess Twilight Sparkle, pony researchers discover something remarkable, a special substance that, when modified just right, has the capabilities of embedding magical ability within non-magical creatures.
This discovery leads to Seaquestria being the first chosen location for the testing of this new magic, causing a blossoming of culture within the underwater kingdom, but of course... things go wrong.
When a pony named Bluejacket finds himself in the fallen city, he discovers a submerged maze of crazed ponies, spell flinging griffons, and murderous magical mechanicals.