WMG: Sonic.exe

Warning! Spoilers ahead!
Sonic exe is an alternate Fleetway Super Sonic.
A sadistic psychopath trapped in the form of the blue blur? Adding the creepiness factor, Sonic could originate from the infamous bad ending of Sonic 2, where it's implied Dr Eggman killed Tails. If so, perhaps the extreme rage coupled with the Chaos Energy created Sonic exe?
  • But then Tails wouldn't be around for Sonic.exe to kill in the original story.

Sonic exe is actually Kefka.
If you read the story, it SPECIFICALLY describes Sonic.exe's laugh as Kefka's Noblewoman's Laugh — oddly specific, unless it was Foreshadowing. In fact, Sonic.exe is also pretty similar to Kefka when you think about it: they're both Faux Affably Evil, Ax-Crazy, and have pretty serious God Complexes. Perhaps after Kefka got his ass handed to him in Final Fantasy VI, his spirit hijacked the Sonic.exe cartridge, and had Sonic murder his friends For the Evulz.

Maybe this is Kyle's elaborate prank to Tom
Kyle probably knew that Tom is gullible to believe just about anything and that he was a total coward. So what Kyle did was he stayed quiet and didn't speak to Tom for two weeks, got some of his buddies who know their way around making video games to cook up this "haunted" Sonic the Hedgehog computer game with all these stolen assets from other video games that would scare Tom like a kid watching Friday the 13th, had someone else to make the bloodied stuffed demonic Sonic doll, and another person to pose as the mail man to ship the CD to his mailbox. Kyle, lurking somewhere around Tom's house, plays the waiting game until he finished the level with Dr. Robotnik, where he then sneaks in Tom's room like a ninja to plant the doll on his bed, took out a voice-changer so he'd sound demonic and screw with him at the last minute.