Really it's only purpose is to make Megas available... Anyway, randomly you'll get vouchers- legendary vouchers are the rarest. With these vouchers you can get random mega stones that you can transfer to Pokemon Vault to get Mega Pokemon.
I know that not every Mega Stone is in this game, some Mega Stones correspond to pokemon not available in Vault just yet. They'll be added as soon as those pokemon are added. June 2: Sablenite Added October 20: Altarianite Added October 10: Bug Fixes October 9: Released.
