Illusion of Gaia/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 Nuclear Weapons Taboo, it simply couldn't be said out loud.

Will is a reincarnation of The Blazer. And in turn, 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...

The Tower of Babel is a Space Elevator.
Think about it. It's a tower that literally rises up into space. In the 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). Applied Phlebotinum 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 Tower of Babel: 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 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.

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,  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 Green Aesop ending could be an extension of Will's concerns about the environment (perhaps he enjoys Ranger Rick). 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 All Just a Dream, especially with no obvious hints of that being the case unlike with most examples of that trope.