Illusion of Gaia
The comet is completely made of radioactive materials.Whenever it passes Earth, its "light" either horribly mutates people or gives them superpowers.
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, 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 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.