[[WMG: The comet is completely made of radioactive materials.]]
Whenever it passes Earth, its "light" either horribly mutates people or gives them superpowers.
* It probably was, considering the NuclearWeaponsTaboo, it simply couldn't be said out loud.

[[WMG: Will is a reincarnation of [[VideoGame/SoulBlazer The Blazer]]. And in turn, [[VideoGame/{{Terranigma}} Ark]] might be a reincarnation of Will.]]
The three games deal heavilly with reincarnation. And while Will->Ark is stretching it, there are enough paralells between the Blazer and Will if you equate the ruins in Illusion of Gaia with the different areas in Soul Blazer. Furthemore, Solid Arm states that Will reminds him of the Blazer.
* Well, the games ''are'' "Spiritual Successors" to one another...

[[WMG: The TowerOfBabel is a SpaceElevator.]]
Think about it. It's a tower that literally rises up into space. In the [[http://vgmaps.com/Atlas/SuperNES/IllusionOfGaia-TowerOfBabel(Unmarked).png top-left]] image, the top of the tower is clearly so far up that you can see the outline of the planet and the horizon. The original civilization (Babylon?) that built the Tower and made use of the Comet's light probably used it as a way to access the Comet. This actually explains how Shadow was able to fly off and meet Dark Gaia for battle: he was already free of Earth's gravity (or, at least, mostly free). AppliedPhlebotinum likely explains any issues regarding oxygen and sheer height, as well as how far up Shadow needed to be to take off. This actually fits very nicely with the original idea of the IRL TowerOfBabel: It was supposed to be a way to reach Heaven. Heck, the article on this site even makes a bit of a comparison near the end of the page. How Will could have made it all the way to the top of such a colossal structure likely has to do with [[AlienGeometries how much space is in the tower compared to outside]], as well as the fact that an elevator and a Vampire basically allowed Will to skip whole swaths of the tower's floors.

[[WMG: The entire story of the game is a figment of Will's imagination.]]
It makes sense if you think about it, or perhaps if you overthink it. When the ending rolls around, [[spoiler: we see Will and his friends in an ordinary 1990's school.]] It is as if the events of the game never happened, and that may well be the case: Will may have made it all up in his head while waiting for his friends to get out of class. All the story revolves around Will and the people he knows in his real life, who for the most part are there for seemingly no reason other than to advance the plot (the other characters rarely if ever fight and usually hang around town while Will is doing battle). Some events happen for no apparent reason and aren't crucial to the story in any way, such as Seth's transformation into Riverson; it may have happened that way because Will didn't want one of his friends to actually die in his story (which may also be why they were rarely in danger while Will himself was). The game uses a mutation of Earth bearing little physical resemblance to the original, but retains locations which might be well-known to an elementary or middle school student, like the Great Wall of China and the Pyramids. Most events in the game go Will's way, frequently due to some nonspecific telepathic powers. Even the GreenAesop ending could be an extension of Will's concerns about the environment (perhaps he enjoys RangerRick). The way the story unfolds gives the impression of something raw and simplistic, very fitting for a child's imagination. It would be a rather beautiful use of AllJustADream, especially with no obvious hints of that being the case unlike with most examples of that trope.

[[WMG: The denizens of Angel Village are the descendants of the Mu people.]]
Before the Mu boss fight, Will meets Rama and a few other spirits of the Mu people. They tell the story of a comet-themed catastrophe, which they decided they needed to escape. Having no trees with which to build boats, instead "They started building an undersea tunnel. They dug on, not knowing how long it would take..."
Our heroes end up finding and walking the length of this tunnel, a feat which Neil says took "nearly a month." By estimate of average human walking pace and walking 12 hours a day, that tunnel is around 1,000 miles long. How long would it take for people to dig a tunnel that long using hand tools? Decades? Generations? We know the Mu people successfully completed the tunnel as our heroes emerge from the other end without incident, so presumably the survivors/descendants made it to the mainland and settled there.
The comet is a "weapon of evolution" which causes those bathed in its light to change. The Mu people were bathed in its light and then spent generations under ground. Then, at the mouth of the tunnel, we find a village filled with "angels" who say they're the form that humans evolve into, who live underground because they can't tolerate sunlight. Also, some of the pillar-like statues found in Angel Village resemble those found in the tunnel.
It may as well explain their emotionlessness. They spent possibly a century toiling away in the cold, damp and dark, endlessly digging and working with no basis for time or circadian rhythm, never seeing light or color, eating meager meals of flavorless mushrooms, always with the lingering temptation of turning around and walking back to Mu. When they finally emerged and found they could no longer tolerate the sunlight, they dug straight down where they stood and made their new home, able to manage ambition (a sculptor resolving to build a thousand statues) and yearning (dancing for hours on end in a futile attempt to feel a human emotion, or rushing to be painted with a passionate expression despite all evidence that the artist is a serial killer), yet still living their entire lives without ever laughing or crying. That inability to cry or feel despair may have been the thing that allowed them to survive digging the tunnel, at the cost of joy.

[[WMG: Will and Kara are reincarnations of the Incan rulers.]]
Provided the whole scene on the golden ship involved actual ghosts and was not just a form of elaborate hallucination: Just why do the Incans insist that Will is their king? Did they want to believe it in order to set sails and finally pass onto the afterlife (their duty of waiting for the "king" fulfilled), or is there an actual relationship between Will and the king? If he is a reincarnation, the ghosts might've mistaken him for their king because their souls "look" the same (because they are).
Spinning this further, what if Kara is a reincarnation of the Incan queen? The hair is similar, and it's certainly suspicious how Kara was very fixated on the queen's ring, which also turns out later to be connected to the Tower of Babel (though it could just be that she is an ancestor of Kara).
This could also explain one of Kara's lines early in the game about how she feels "as though we've met before, as if we were good friends". They might have a thing for having to find each other again in a new life...