Ok, so for chocobos, we're going to have this massive cataclysm that opens up a rift in Eorzea. Someone will venture into it and find the great realm of chocobos.
Then everyone will think "Profit!" and thus the mass enslaving of chocobos begins, and there will be enough chocobos to go around. Many will be kept for breeding so we have more when more adventurers get into playing this.
And that's how it will all begin. At least in my deranged mind.