Eberron/WMG

The Mark of Shadow was meant to die, not the Mark of Death, leaving the moon Sypheros ruling over an inappropriate dragonmark and distorting its applications.
The thirteenth moon obviously had a connection to Dal Quor, given the circumstances of its disappearance. Meanwhile, the description of Sypheros, the moon associated with the Mark of Shadow, is suggestive of Mabar. But doesn't that seem kind of backwards for mark associations? Wouldn't it make more sense for the Mark of Shadow to be Dal Quor's, given the similarity of dreams and illusions, and the Mark of Death to be Mabar's, since that's a plane of negative energy? Was the wrong elven mark destroyed, sympathetically leading to houses of Shadow associated with assassination?

The Lord of Blades...

 * ...is the first warforged
 * ... that was made by quori and is inhabited by the Dreaming Dark.
 * ...is the last warforged
 * ...is not a warforged, but a robot from the future
 * ...created by Nemesis.
 * ...or the soul of a giant in an empty warforged vessel
 * ...or the creator of the warforged in disguise
 * ...or the creator who gave himself so many magic grafts the warforged think he's one of them. The rampages of destruction are just because he's so annoyed by the fact.
 * ...or the soul of the creator of the warforged in an empty warforged vessel
 * ...is Bulwark
 * ...was responsible for the Day of Mourning
 * ...and is now the darklord of Cyre.
 * ...is Aaron Stack
 * ...is Jesus in Purgatory
 * ...is a Time Lord. Sorry, couldn't help myself.
 * ...better, is a Cyberman.
 * ...is the Shrike.
 * ... is a Replicant wearing a suit of platemail.
 * ...is an Alchemical Exalt.
 * ...is The Omnissiah.
 * ...is all of the above simultaneously.
 * ...is all of the above, including the last entry, in sequence.

Khorvaire is going to split down the middle.

 * Seriously, look at the map, look at the Mournland, and look at that big glowing chasm in the middle there.
 * So wait, the Glowing Chasm is some sort of magical rift valley, connected to a fault system running up Scion's Sound? Now that you mention it... the world map of Eberron does seem like it could combine into a supercontinent. Maybe even one shaped like a dragon?

The Day of Mourning was caused by:

 * A Cyran security device, set in place with the help of Brelish artificers, who included a secret bypass they could turn on Cyre if things went badly. They didn't think it'd go so wrong though.
 * ...this setup, which deals so much damage that it cannot even be described in scientific notation. A very rough approximation to the damage done can be thought of this way. Imagine that each of the 10^80 atoms in the universe was a universe itself, also with 10^80 atoms, and each of those atoms was a universe as well, and so on. You would need a number of layers equal to the number of atoms in the universe to have enough atoms to write the digits of the damage amount.
 * Someone going overboard with adding feats to the Locate City nuke.
 * Neither of the two damage loops listed here damage objects. The Nasty Gentlemen use damage-linking spells, while Locate City relies on Explosive Spell for its damage output. There's no real way to make objects take Reflex saves, so you can't Explosive them.
 * Are you seriously suggesting that, because an inanimate object has no chance to dodge an explosion, it remains immune to all explosions? That appears to be a bug rather than a feature, one easily repaired by application of common sense.
 * Ravenloft. We know Ravenloft can take in beings from other planes, just ask Lord Soth. We know that both the Mournland and Ravenloft are known for Ominous Fog. We know that when Ravenloft takes in a new Darklord, it tends to haul in a significant number of people for standing too close, i.e. however close the Dark Powers think is too close for that specific one.
 * Karrnath/Kaius. Note that the Mournland doesn't impede undead, Cyre and Karrnath were at war when the Day of Mourning hit, and vampires are associated with mist/fog. Either this was a weapon Gone Horribly Right or, like Ozymandias, Kaius is willing to sacrifice a lot of people for peace. Either of these would explain why Kaius is of evil alignment.
 * Whatever it is, something intelligent definitely had some manner of control over it. No event of random chance would match Cyre's borders.

The nature of the Draconic Prophecy

 * The Prophecy is an allusion to the Abrahamic God and similar "omniscient" entities. Conventional omniscience is, scientifically speaking, impossible. It would, however, be theoretically possible to know the probability of every possible event, and how these probabilities interact with each other. It would then be impossible to make hard and fast statements about the future, but it would be possible to make predictions. Predictions based on such a 'partial omniscience' would roughly take a format of "If X, then Y". This closely mirrors the Prophecy.
 * This concept has existed for a while in the real world and is generally known as Laplace's Demon.

The bodies in the Mournland are still alive.
The Mournland contains thousands of bodies which have remained utterly still for years and have no pulse, breath, or heartbeat. Therefore it's assumed that they're dead. But they haven't decayed at all, and none of their equipment has corroded. In fact, there's no sign of the passage of time on the bodies at all. So it's possible that they're actually still alive, but somehow frozen in time.
 * That's going to make the few who were ever buried very pissed.
 * Assuming it's not just a permanent gentle repose effect.