The game's Steam page has a section titled "Canon or headcanon?", which reads as follows:


This is a reference to an infamous tweet made by the Sonic the Hedgehog Twitter account in response to a tweet from the Puyo Puyo Twitter account showing off art made to commemorate Sonic's inclusion in Puyo Puyo Tetris 2, where the Sonic Twitter account claimed that "Everything is canon". According to the IDW comic book series' lead writer Evan Stanley, The Murder of Sonic the Hedgehog is considered non-canon outside of a few references in the IDW comic book series after the game's release, but the series' associate lore manager Chris Hernandez later claimed this was not set in stone.

Early plans for the game had Charmy Bee and Cream the Rabbit involved in the game's plot, but these were scrapped as the devs felt that they were too young to participate in a murder mystery party game.

The 8-bit version of Sonic the Hedgehog 2 has two endings:

• A good ending, played if the player collects all the emeralds, where Sonic and Tails run off together at night, and see a constellation in the shape of their heads in the sky.
• A bad ending, where Sonic runs alone in the night, and sees a constellation in the shape of Tails' head in the sky

Although it has never been confirmed, many fans have speculated that the bad ending is supposed to involve Tails dying at the hands of Dr. Eggman, with some even going as far as to suggest that a large star on the right of Tails' forehead is supposed to represent a gun wound. The @sonic_hedgehog Twitter account has jokingly acknowledged this theory without confirming one way or another if it is true. Once in a cross-promotion for The Murder of Sonic the Hedgehog and the 8-bit game's addition to Sonic Origins Plus, where it compares both games' inclusion of "a beloved character's possible demise", and in a piece of promotional artwork taking place at a carnival, where Tails gets nausea on an intense ride and his constellation can be seen above him, with the "gun wound" star being placed on his muzzle.

The game's protagonist does not have an official name, as they are meant to be a representation of the player. However, both promotional material and the game files refer to them as "Barry". Additionally, writer Ian Mutchler has confirmed that their intended species is a quokka. As such, fans have taken to referring to the protagonist as "Barry the Quokka" when referring to them.

In The Murder of Sonic the Hedgehog, when Sonic is found presumed dead on the ground, the pose he is laying in is a reference to a meme within animation circles known as the "Family Guy Death Pose". This pose is frequently used throughout the animated series of the same name created by Seth MacFarlane, which became criticized in later years for utilizing cheaper animation. This is not the first time this pose was referenced in the Sonic the Hedgehog franchise; the first time being in Issue #3 of the IDW comic book miniseries "Sonic the Hedgehog: Imposter Syndrome", where the character Surge collapses into the pose at one point.