Ending, plot discussion. Warning: Spoilers

[NoloeTazier]

Two things.

First,
I'd like to nip in the bud that theory of the 12 not existing. They aren't just a cage for Bahamut.
Case in point: prayers during the invasions gave buffs and debuffs based on who you prayed for.

Second,
I agree with this idea that perhaps atomos might work for bahamut.
Why? The invasions. They had deepvoid enemies. Minions of Atomos.

Perhaps he was redirecting the aether from the aetherytes towards bahamut in order to empower him.

Not 100% sure, just think its a viable explanation for Atomos and the deepvoid monsters throughout the invasions.

Atomos works for no one, he only does what he does. Deepvoid monsters are beings that follow him through the void he creates as he switches dimensions/plains. If Atomos was working for Bahamut, he would have appeared sooner in the storyline than when he did, he only appeared when the aether flows themselves began to become unstable as Dalamud sapped at the aether.

Just because magical things begin to happen doesn't mean it automatically gives proof to The Twelve. The Twelve "altars" were just too perfectly positioned around Eorzea for me to say this was divine intervention. They were practically a circle with the Tomb of Xandes (the altar in Mor Dhona, also associated and near The Crystal Tower and the tomb of an Allgan king) right in the middle. That sounds more like a weapon to me than some entities watching and moving pieces around like chess. The Twelve could have easily existed in the past, Twelve people who sealed Bahamut the first time, of which some went and founded Ul'dah, Limsa Lomina, Gridania, and Ishgard. I can easily see the stories being passed down and the true understanding of these people raised to the form of gods.

[Majidah]

Atomos works for no one, he only does what he does. Deepvoid monsters are beings that follow him through the void he creates as he switches dimensions/plains. If Atomos was working for Bahamut, he would have appeared sooner in the storyline than when he did, he only appeared when the aether flows themselves began to become unstable as Dalamud sapped at the aether.

Just because magical things begin to happen doesn't mean it automatically gives proof to The Twelve. The Twelve "altars" were just too perfectly positioned around Eorzea for me to say this was divine intervention. They were practically a circle with the Tomb of Xandes (the altar in Mor Dhona, also associated and near The Crystal Tower and the tomb of an Allgan king) right in the middle. That sounds more like a weapon to me than some entities watching and moving pieces around like chess. The Twelve could have easily existed in the past, Twelve people who sealed Bahamut the first time, of which some went and founded Ul'dah, Limsa Lomina, Gridania, and Ishgard. I can easily see the stories being passed down and the true understanding of these people raised to the form of gods.

The old elvaan said we were using only part of the power of the twelves because summoning the dieties entirely would lay waste to eorzea's energy. Or something along those lines.

Also the Archons are the reincarnation of the 12.

The praying stones could have been placed strategically? Sure.
Is it a more effective way to be heard by the 12 than praying anywhere? Of course.

But lets not fall in the egg and the chicken. The 12 came first. Maybe it was the Allagans who created the praying stones in order to channel the 12's power into a cage.