Chocobo's Crystal Tower was a flash game developed by Square Enix playable as a Facebook app. The player could raise a chocobo, battle monsters to earn gil and then customize their chocobo with unique accessories. Players were able to look after each other's chocobos and different players' chocobos could mate with each other.

An evil wizard called Evilzard had summoned the Meteor of the Apocalypse, but a brave hero shattered the Meteor and save the world. The Meteor shards fell across the land, spawning an intricate network of towers and dungeons. Monsters crawled out of the towers, spreading fear. Many adventurers tried to destroy the monsters and the towers, but a black curse left by Evilzard before his death prevented them.

One day, a chocobo emerged from one of the towers, heavily wounded. It had ventured inside and vanquished the monsters within, because the tower was silent. This chocobo, Boco, was hailed as a national hero of Enisque, and since then, the kingdom of Enisque started a chocobo breeding program, sending chocobos into the tower one after another. The program was a success, and novice royal chocobo breeders have since come in droves to breed and train the chocobos to continue their quest to destroy the towers.