The prophesy has been cryptic and many parts turn out to be not what they seemed.
With Atomos seeping black doom from the hells, they do bring with them Overaspected Crystals. The biggest problem facing Eorzea at the moment seems to be the draining of aether from the planet itself.
Could Atomos be replenishing the aether, but his only way is to bring forth these terrifying cratures to ferry it?