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The music from Ice Cap Zone is actually a remake of an unreleased song from 1982, "Hard Times" by The Jetzons, a band co-composer Brad Buxer was apart of.

SEGA originally hired Michael Jackson as composer for the music on the game but later dropped him over the infamous allegations of child molestation. However, his song writing team carried on without him and it is believed that part of what he had written remained in the game. There are notable similarities between the music recorded for Sonic 3 and music from Jackson's previous recorded tracks from the Dangerous album, and a track from the later released HIStory album (which was composed during the time of the game). For example, there is a sample in the Carnival Night Zone's music that is taken directly from the song "JAM" and the credits theme parallels Michael Jackson's later song, "Stranger in Moscow".

This game features the first appearance of Knuckles the Echidna, who became phenomenally popular, and in many fan circles is even more popular than Sonic himself. He went on to become as much a main character as Sonic, Tails and Eggman.

This is the first game in which the player is able to control Tails' flight ability. If there are two players, Tails can give Sonic a lift and carry him over short distances. He can also swim, though he cannot carry Sonic whilst doing so.

This is the first Sonic game that gives you ability to save your progress.