I think the Magic Realm, pretty solidly. The "mythos" is not, per say Evil, "just" dangerously Alien, and that is the Magic Realm. The heightened awareness that comes from being in a Magic Aura is canon to the "mythos" as well. Now, the small gods of Earth are probably Faerie........
Any of the realms. Or none or a 5th if you really wanted to play up the beyond comprehension. It also might depend on the exact being.
Divine: Isn't one of the Mythos creatures dreaming the universe? Also incomprehensible? That sounds like the Divine!
Infernal: Warping and destroying the world. When it awakes it breaks the minds of mortals. Cultists engage in human sacrifice to it. That's infernal.
Faerie: You want to know what can be faerie? Anything any human can imagine. Such creatures wouldn't fit truly into the Mythos since they are not actually incomprehensible. They also do care very much about humanity much unlike the Mythos creatures. However a human would have difficult telling the difference between a Faerie faking not caring and incomprehensibility with the real thing. They would look like a Lovecraftian creature to us.
Magic: Alien and uncaring. This is a good fit for these creatures.
No Realm: These are creatures of advanced Experimental Philosophy. They are insane combinations of new fundamental elements, ingenious combinations and connections of Sympathy and contagion and the like. While the effects are totally natural you have no hope of understanding how they function. They understand the universe on a fundamental level and that makes them extremely powerful. This has the added benefit of making them seem Godlike. There powers go through any resistance and can't be countered. Just like miracles.
Fifth Realm: I would call this the realm of Truth. The other four realms are mere reflections of humanity. Their belief in ideal forms. Their dreams and hopes. Their belief in something greater and their purest emotions. Their belief in something baser and their basest emotions. The Realm of Truth is like the Divine Realm except more incomprehensible, more powerful and uncaring of humanity. These guys control the universe on a fundamental level. They control fundamental laws, can violate seemingly inviolable limits and generally be extremely strong. Make sure to show the Divine failing in the face of this. Abandon all hope.
I could see them being a mix of all the realms, but one of the main things is that they are alien. The ones that notice humanity and desire something from it though I would think they'd need to be Divine (only a few of those), Infernal (again, only a few) and Fae (most of the rest).
The ones that are utterly incognizant of humanity would be Magic as would their servants IMO, as Magic is strongest in the most secret and secluded places of the world/universe. The ones that are involved with humanity in some way I would say are also affected in return by humanity, with the Fae being the most impacted. And I definitely think Nyartolep (don't correct it, I know I spelled it wrong ) would be a powerful fae.
Aquam regio with a doorway to an Aquam vestige that is not only inhabited by a giant squid-thing but IS a giant squid-thing. Sounds like reason #3 for 'why harvesting Vis from the ocean floor isn't actually that clever'
OOOH! Lovely stuff to hit my Criamon player with in my Wednesday night game. He wants to play around with exploring far reaches of the magic realm. I must go back and read "The Gate of the Silver Key". Massive, imponderable intelligences that he will end up praying that they don't notice him. MWA-HAH-HAH-HAH!!
Oh heck yes. And do some research on the "early days" of the Cthulu timeline. Nyarlathotep appears as an Ancient Egyptian Pharaoh, in the Lovecraft canon, and gosh, in the Ars Magica canon, there was a big war between the Magic Realm and the Fairy Realm at about the time of Ancient Egypt, a war that caused the loss of a lot of magic....
So have your player find evidence that the Great Old Ones are the great Gods of Magic worshiped by the Egyptians before the breaking of the Old World. The Order is founded on a lot of old Egyptian/Greek Rituals, and the beliefs of House Criamon fit very, very closely the beliefs of many "cults". Coincidence, or is Twilight the door by which the Great Old Ones are coming back? Is Final Twilight a joining with them? Is ever point of Warping (which, after all, is a taint on the Natural World) bringing our World close to them?
What does he do with such a thread? Ignore it and possibly Damn the World? Pull it, at the risk of his mind, and the possibility of ending his House, and maybe the Order?
Alternately, the Order as it is currently portrayed can actually BE a Cthulu-type cult: it's just that we're seeing it from the perspective of the Order, rather than of the mundane (medieval) investigators.
The uneasiness normal folks get in an aura? The fear and loathing they get around magi? Strange and degenerate mutations of covenfolk, who live out in remote locations and serve their eldritch masters? Obscure and obscene Initiation rituals done when the stars are right? Remote and uncaring entities whose very presence can destroy (warp) your body and mind? Change the assumptions of the players, and the lighting/mood of the story, and CoC is just Ars Magica from a grog's perspective.
Of course, it's not a complete 1:1 mapping - the Divine does exist, and there are other forces at work as well. But if you squint at it a bit, and emphasize the inhuman aspects of the Magic realm and the warping effects that high-level magics cause, then it's at least a good inspiration for some interesting stories.
I considered that - the modern interpretation of that would be Kierkegard's "Fear and Trembling" theology. However, that would pretty much go against the stated claims of the Divine in the RoP books, which is for the betterment of humanity. Also, in terms of game mechanics, Divine warping/Ascension(?) is actually kind of good for you. (It takes you a way for a bit, but you come back wiser for it, and it doesn't kill you.)
In contrast, the Magic realm is the only realm that simply doesn't care one way or the other - which is one of the main defining characteristics of Lovecraftian horror. (the Incomprehensible + uncaring nature of the universe).
The Infernal realm would be about as incomprehensible as the Divine - it's just that a small part of the difference is understood. (The question as to who is in charge.) but other than that, they're just as incomprehensible as any other eternal, unchanging innefable spirit. This would also go against how the Infernal is portrayed in the RoP books - they are actively malevolent. Specifically, they will not choose to do a selfless action. An entity who is pushing Freedom wouldn't have a problem with a free choice that benefitted truth, justice, and the well-being of others. Demons do have a problem with this. Thus, while they are free, they will never choose to be good. Which I would argue is part of their own innefable nature (that stems from existing outside of time, but that's just a personal take on the whole thing.)
As such, I'd argue that the only one that is possible to understand are the Fae - and they're just as complex as any human creation. Which is to say, you can probably wrap some general parameters around them, but the devil (as it were) is in the details.
The Divine is certainly incomprehensible. Jesus was not God. Jesus was God. That's cannon Divine. On top of that it seems outright malevolent. It shattered the Tower of Babel, its personally responsible for aging and death.
Now there are reasons why the interpretation of infernal=freedom isn't wholly correct, but that's besides the point. Sure demons may be always chaotic evil, but what about demon blooded characters? Their infernal, but they aren't evil.
More to the point, the characters don't actually need to be right. That's what spin is for.