Inari and the head priest are gods. The head priest is concerned with maintaining creation, Inari has the power of creation and destruction (as represented by the beads and the hammer respectively, and is perturbed having created life, that life would continue and create itself without his action, thus making him unneeded. His power becomes a burden to him. Buddha creates Koto to soften Inari's heart with the power of love.

On a whim, under the influence of Koto, he decides to save Yakushima, creating first the two siblings, and the mirror Kyoto, to make him 'happy'. He also transfers to him the divine power of creation. Mirror Kyoto is a forbidden thirteenth plane, connected with the others, such that damage done to mirror Kyoto is also done to the entire multiverse. Koto foresees destruction if she remains in Mirror Kyoto, and so they both leave. Yakushima resists the power - he is angry already about the whole immortality thing, he doesn't want the power of a god as well.

Later Inari has a child with Koto (Koto2). Koto2 inherits from Koto the borrowed existence from the Buddha, and so forces Koto to reside on the moon. Inari is disgusted to see the creation of life not directly by his own hand, but over time becomes fond of her, conferring upon her the power of destruction.

By chance Koto2 gets to Mirror Kyoto, causing damage to the fabric of all of reality to enable her own entry, and so that Koto could be with them. Thus she fulfils the terms of the prophecy.

Seeing Koto2 threaten the entire multiverse for the city created to make Yakushima happy, Inari is convinced that there is no longer any particular reason to hold any loyalty to his brother and maintain the world. Forcing Koto2 to destroy Mirror Kyoto, and therefore the multiverse, he compels Yakushima to decide - either take on his responsibility and so the power of creation, or get what both he and Inari want: death.

TL;DR Inari is an arse, this is his way to retire.