Eternal Darkness/WMG

Mantorok opposes any sort of killing or enslaving of humans.
In the Something Awful LP of this game, user Antilles posted this: "Mantorok is the god of chaos, right? IMO, between exterminating/enslaving humanity and letting us do as we wish, the latter choice is the most chaotic."
 * That was already in the game's story. If you payed attention to the pictures in the first play through of Mantorok's temple it states Mantorok acted as a fertility god to the ancient people in Cambodia.
 * Though, really, that could have well involved enslaving those people. They built his temple and fed him flesh, after all.
 * Maybe but Pious states Mantorok was reduced to eating flesh after being bound.
 * Mantorok is a very patient Corpse God. Which is why he's worshipped as a fertility god: rotting things make for very fertile soil. Being that Mantorok can see through time and reach across timelines, so humanity is all at once alive and dead and constantly dying to him. Probably a sweet deal.

Humanity is Mantorok's horrors.
Another S.A. user had this theory that humans are in fact created by Mantorok. Humans die easily but create unprecedented amounts of damage with weaponry. Just as Mantorok rules over all, humans can use all magic with the proper runes, unlike the others who are stuck to one alignment. The bonethieves were created to destroy Mantorok horrors by hiding from within. "Also, the reason why all the gods intend to make an example of humanity if they win? They're doing it to spite Mantorok."
 * For that theory to work, humans would more likely be Mantorok's guardians.
 * Of coarse that doesn't work either, the ending achieved after beating the game on all three alignments states Mantorok just manipulated some people to do his work since his binding prevented him from calling on his guardians. Humanity is just a substitute.

The zombies in Eternal Darkness aren't actual zombies.
Rather, they're Guardians that take crude humanoid shapes. The zombies look nothing like the actual human corpses the characters encounter, can be summoned up from anywhere, and display abilities that human bodies really shouldn't have. What sort of corpse can regenerate lost limbs and heads, or replace them with green shadows?
 * Zombies, by definition, are dead bodies reanimated by super natural powers (Except in real life they aren't really dead and no powers are involved). They don't have to look like corpses, that idea was codified by the book Night of the Living Dead.
 * I always thought it was rather funny how Mantorok Zombies continue to show up after Pious' chapter. Shouldn't Mantorok be doing anything except threatening his Chosen (even if his Zombies are a cinch to defeat)?
 * The point isn't to threaten them, but to test them. Gods just do that sort of thing. Read the Bible or whatever religious book of your choice. The Chosen ones of God (or the Outer Gods) always had the hardest tests to overcome.
 * Or it has lost control over the zombies due to its binding.
 * Or it could be because Mantarok's zombies are the only ones that almost definitely are actual zombies. They're ancient skeletal mummies, but unlike the others they're commonly seen lying around before something disturbs and awakens them. It's likely that they, and all the monsters, are autonomous of their creator and so are just trying to guard certain places, or kill all living things, without the ability to identify the Chosen.

333 is very significant in the game
No duh, but in the first part of the game, after Alex wakes up from her nightmare, the clock reads 3:33, and in the Roivas Household, you are supposed to change the time on the grandfather clock in the library, if you fail 3 times, a ghostly whisper (Mantorok) tells you the number is 3:33, also, if you multiply 333 by 2, it becomes 666, familiar?
 * Also notable are there are 3 Ancients and 3 Roivas, each Roivas seems to be similar to each Ancient in terms of their meters, Alexandra Roivas has the most sanity (Xel'lotath), Maximillian Roivas has the most health (Chattur'gha), while Edward Roivas has the most Magick (Ulyaoth).
 * Strangely, the Roivas family reversed the natural pattern, normally, Ulyaoth takes down with Chattur'gha with his Magick, Chattur'gha takes Xel'lotath down with his power, Xel'lothath takes down Ulyaoth with her insanity. But the flow was seemingly reversed, as Maximillian, the most powerful, was taken down by insanity, Edward was killed by the power of the Ancient, despite being the most knowledgeable at magic, and the final blow, Alexandra went into a Heroic BSOD with the knowledge that she just released another god that could destroy the world, and she's the most sane out of the 3.
 * So, the Ancients are the Invisible Clergy?

The ancients were at some point human, but Mantorok converted them to become his minions, which horribly, horribly failed.
Eh, just felt like making this theory, get someone else to do this...

Okay, I'm not lazy anymore, at some point, the Ancients were humans who excelled at something better than other humans, Chattur'gha was a man of power, but a man of war as well, wanting nothing more than it, Ulyaoth excelled at magick, drowning himself in this desire to become more powerful and more knowledgeable, whereas Xel'lotath just went nuts, and just became more and more unstable, the reasons they can be beaten, Ulyaoth can beat Chattur'gha because knowledge is power, Xel'lotath can defeat Ulyaoth because that's a little too much knowledge, and Chattur'gha can defeat Xel'lotath because they were former lovers (Which may be the reason Xel'lotath "just went nuts"), his real love was war.

Mantorok decided to collect these three and convert them into gods PAINFULLY, they served him willingly for a while, but their memories returned, rediscovering their hatred for each other, Mantorok sealed them away, but he knew he could get them to destroy each other should they ever be released.

This piece of work is a stab at what the ancients might have looked like if human.
 * The portraits with the effigy stands in the gulf war chapter could also be what they looked like.

There is a fifth ancient.
Confirmed by the creators, but the spells it has seem to affect the environment, so it would probably be a reality warping Ancient.
 * Either that or a narwhal

Mantorok, in destroying the other Gods, has doomed himself to his sealed chamber for eternity
Think about it. Pious sealed Mantorok using the power of one (or was it all?) of the other gods. Now that Mantorok killed all of them, no one is left (with the possible exception of the aforementioned reality warper) with enough power to free him. 9 pargons indeed.
 * Which may be what he intended all along-he wants to die in peace.

The fifth ancient is the one that organized the relationship between the others
In the beginning, this entity created the others for unspecified reasons; however, Ulyaoth, Xel'lotah, and Chattur'gha started causing problems, so the entity sealed them away and left Mantorok to keep things in line. Either it trusted Mantorok to be able to handle anything that could have happened, or it was too far advanced to care either way (it would effectively be to the ancients what the ancients are to man).
 * If the fifth Ancient's bailiwick is the environment, it may represent the very rules and laws that make up existence, an abstract concept that binds the others together - the "paper" on which the "rock-scissors-paper" diagram is drawn.

Pious the Lich was working for Mantorok all along.
It's possible that even he didn't know about it, but Pious was clearly intended to be one of the Chosen Ones. Mantorok probably arranged for him to join up with the Ancients, work for two thousand years trying to free his master, only to make him to lose at the last possible minute, destroying the essence he holds and ensuring his masters death. When you see Mantorok's scheme to make the Ancients destroy each other, it becomes very, very likely he arranged something like this in order to get his plan to work.
 * Plus, when you start a new game +, it's impossible as Pious to pick up the essence of the gods you've already beaten... A gaming schtik that can very well be Mantorok manipulating the events so that the three possible outcomes happens, and thus ensuring the common destruction of the Ancients as seen in the real ending.

Din, Farore and Nayru are related to or are the same entities as Chattur'gha, Ulyaoth and Xel'lotath.
They share a color scheme and there is a similar balance of power in both groups, both are incredibly old and considered the gods of their respective worlds as well. Assuming LoZ and Eternal Darkness take place in the same universe then it's not much of a stretch that the three goddesses and the three ancients could either be the same or similar entities.
 * Chattur'gha is the god of Physical Strength, where Din is the goddess of power. There is more to power than muscles. Ulayaoth is the god of knowledge but again there is a difference between knowledge and wisdom which is Nayru's domain. Xel'lotath is the goddess of insanity contrasting Farore goddess of courage because a brave person will do things where others would be too scared but an insane person will act beyond all reason. Also, while the goddesses of Zelda work together, the ancients of Eternal Darkness work against each other, so they are a bastardization if anything, definitely not the same.
 * Which makes the Eldritch trio into a kind of Anti-Triforce, each opposing what their respective counterperts stand for.
 * Sooo that makes Mantarok the Fourth Triforce Piece?
 * Mantorok is Ganondorf' counterpart, Ganondorf seeks to obtain the Triforce's power while Mantorok seeks to destroy it.
 * Funny, I saw a similar connection to the three elements of starter Pokémon: Grass/Xel'lotath beats Water/Ulyaoth beats Fire/Chattur'gha beats Grass/Xel'lotath.
 * I see it more like Dark/Xel'lotath beats Psychic/Ulyaoth beats Fighting/Chattur'gha beats Dark/Xel'lotath
 * Actually, Xel'lotath would be the Psychic one, she has power over the mind. And though those do correspond to the actual patterns, I think that what the top poster was referring to were the colours.

Mantorok simply destroyed the other Ancients out of a sense of duty
It's established that Mantorok's role in the pantheon is to keep the other three in check. When Pious Augustus condemns him to a slow death, he's weakened too much to continue to seal them... so as a last-ditch effort to complete his task, he kills them instead. Yes, he is stated to be plotting something in the "true" ending, but this is actually unrelated -- he can just move on with whatever he has planned now that he's completed his obligations as the keeper and overseer of the Ancients.

Mantorok's plan is to kill off the yellow Ancient
Related to the above, this is what Mantorok's unrelated scheme is. Now that he's dealt with his duties, he plans to kill off his equal and opposite number, mentioned in Word of God. Whether he has malevolent reasons for this, or it's simply so it won't be left unchecked when he inevitably dies is unknown at this point.
 * It would make perfect sense if the fifth Ancient represents Order to counterbalance Mantorok's Chaos, as is speculated below.

Pious fell to the Ancients because he was too hardcore

 * Pious was a veteran commander and grew up in ancient Rome, both things that tend to nurture badassery. Whenever anyone else came across Guardians or other supernatural horrors, they went insane, but to Pious the Guardians were just some particularly ugly bitches to open up a can of whoopass on. Unfortunately for Pious, the same easily-terrified nature that made other people go mad at the sight of eldritch abominations warned them that the essences of the Ancients were to dangerous to touch. So, where everyone else (rightfully) pussied out and wrapped an essence in something before picking it up, Pious just grabbed it, and wound up lichified.
 * People do not go insane by looking at the enemies of Eternal Darkness. People go insane when the enemies of Eternal Darkness look at them. They are purposefully draining your sanity to make you easier to kill so they purposefully chose not to do the same to Pious. Though as an experienced soldier Pious may be immune to the other ways the game makes you lose sanity(killing innocents) so its likely they chose him to take the artifact because he is used to following orders and has no problem with killing those who get in his way.

The Yellow Aligned Ancient represents Life and Order

 * But taken to horrific extremes. Such as turning people into mindless immortal vegetables in order to ensure tranquility.
 * Contrawise, it may be speculated that Mantorok represents both decay and fertility in the same sense that insects can enhance and digest decay to return crucial nutrients to a forest ecosystem. Mantorok corrodes the universe to ensure that its material can be used in the birth of a new one. As such, the Yellow Ancient is opposed because it represents stasis. Within the context of this theory for Mantorok it would appear that the Yellow Ancient does not represent life, per se, but rather a state of changelessness beyond life and death. Think gas clouds and heat death.
 * This makes a certain amount of sense; the magic system is all based on an immutable noun-verb system. If the Yellow ancient governs order, it would explain why not all the combinations of runes work, even if logically there's no reason they shouldn't be able to produce some effect (Project+Self, Protect+Object, Dispel+Creature, Summon+Item, etc). Also? Yellow and Purple are complementary colors, the color theme would make sense for them to be opposed.

The Ancients aren't targeting humanity-at least, not in the game.

 * The Ancients are very aware of the various realities and timelines, including the one that exists outside of the game disc. Knowing that the humans they will face will be controlled by a being beyond the borders of their universes, they try to prevent him from playing the game by convincing him he is insane...or that his memory card is erased.

The What Could Have Been entry refers to two unsuccessful bearers of the Tome of Eternal Darkness.
A Knight Templar and some person that has all the equipment for another character... they could be interpreted as two of the possible tens or hundreds or thousands of unsuccessful Chosen that we didn't get to play as because they failed. Constant arm-breaking punching out the Ancients unfortunately makes a lot of sense...

The Pillar of Flesh is a sacrifice to Mantorok
We know that Mantorok is forced to eat humans to survive and we see him eat two monks with the worms in Ellia's chapter.The pillar of flesh is built over a sort of purple mist (the color of Mantorok magic), and the worms that come up from the mist to eat the slaves look just like the worms that eat the monks earlier. I'm not sure why Pious would sacrifice to Mantorok, though he does have to make sacrifices to the Black Guardian to keep it bound, so maybe he has to feed Mantorok to keep it bound as well.

Dimentio is Ulyaoth.
I played Eternal Darkness first, of course, but just looking at the character sheet for Ulyaoth after having played SPM made me laugh... and then be mortified at the idea. Alternately, he's Xel'lotath after going even more crazy as a result of whatever rites or process turned him into an Eldritch God-figure.
 * Xel'lotath is a girl, dude. Unless you think he BECAME a girl after whatever his ultimate fate was at the end of Super Paper Mario.

The Ancients are all legendary Pokemon
Red beats green, green beats blue and blue beats red, all of which are beaten by purple (dragon types). Sound familiar?

Mantorok is an apsect of Waluigi
W

The Darkness is a black ancient.
Who's to say there aren't plenty more ancients out there?
 * And Jackie Estacado is his Herald

Dr. Lindsey had fought Eldritch Abominations before

 * It's why he's so prepared to fight monsters and has such a high sanity meter. He's already dealt with these things and for him the Ancients were just a regular Tuesday.

The detective in the beginning was Pious in disguise.
I can't get over two things about the detective: a) his creepy eyes, and b) a line he says: "It's a shame we couldn't meet under brighter circumstances." A) might just be the graphics, but B) always seems too suspicious to me. It makes a certain bit of sense, especially if you believe the WMG about Pious working for Mantorok all along.

Actually, rethinking the eyes, the detective was almost certainly a bonethief if he wasn't Pious or the Fifth Ancient.