It comes from the depths of the Darkhold

[Anonymoose]

I don't understand Atomos. It manipulates time/space. It can summon monsters from the void. What keeps it from just making everything not exist?

Usually, Atomos isn't working of its own accord in the FF-verse. It has been used as a summon previously, and in FFXI it was performing the bidding of The Goddess Altana through the Cait Sith (eating away the True Future, where the Crystal War had continued until both aggressors mutually destroyed each other and the world, leaving only the contents that would create the future we played in).

Now, in Vana'diel, Atomos actually gets to decide which future continues to exist when they come to a head - this could be what's going on now.

Let's return to the Prophecy of Mezaya Thousand Eyes:

Ne'er till land consumes sun can sea bear moons.
Heavens spew crimson fire. Hell seeps black doom.
Stray seeds quicken in ash's grey embrace.
Valiant blades forged under the Twelve's good grace.

When the sixth sun (Sixth Astral Era) sets, the seventh moon is revealed (Seventh Umbral Era, ushered in by water - seen in game as a great deluge of rain; remember those?). From the sky comes fire (Meteor; Dalamud), and the void spills black dooms (unnatural enemies). In response to this, "Stray Seeds" (powerful individuals from all over the world; The Archons - Louisoix, Y'shtola, Urianger) are brought to action, their intervention intended by The Twelve themselves (each seems to represent one of them).

Perhaps the Atomos were summoned by Louisoix for the same purpose, to prevent the future we're destined for, consume it (returning it to the void), and land us somewhere else in time until this can be dealt with. When you defeat an Atomos, you're left with a Voidstone - which sometimes reveals that the world around it is becoming distorted, giving some weight to this theory.

Though, this has some negative side effects - the rapid consumption of aether to one area overaspects all crystals, clusters, and gates, and the connection between Eorzea and the Void allows even more creatures to spill through.

That's not a big threat compared to total annihilation via the empire, especially since when it gets out of hand we can take down both the Voidsent enemies AND the Atomos that has gone meltdown.

[Rau]

iirc The Void is spread across the entire Final Fantasy Universe? I believe that is a plot point in the Dissidia, but not sure if that is "canon"