This is the first time I've heard of this. Can someone please explain to me what's going on?
This is probably the best summary I can surmise on my own:
1) Sonic Team is crunching to deliver Sonic 3 and by this point have already had to split the game in two to get something out the door by the release date. Also, the sound code is buggy. (This is all from the Sonic 3 prototype)
2) Sega of America decides the solution to this is to bring in Michael Jackson's sound team - the most notable of which is Brad Buxer, who will be important when the music rights stuff hits the fan 20-some years later.
3) Said sound team, allegedly, produces a completely all-new soundtrack for Sonic 3.
4) Work is then done, at a VERY late stage in development, to bring this music into the final game.
5) In the VERY short timeframe this music was being implemented, Jackson and Sega had a parting of ways for unconfirmed reasons.
6) At this point, Sega CLAIMED Jackson sound team's music was removed from the game
7) But it's clear going by how similar Sonic 3 credits is to "Stranger in Moscow" that there's traces of it.
8) There's speculation for years about what music is Jackson's music, but in retrospect it's pretty obvious, because....
9) At some point in the latter 90's, Sonic & Knuckles Collection comes out for PC with some Sonic 3 music tracks different from the retail Sonic 3. Initial speculation is that the tracks could not be replicated in MIDI correctly.
10) Meanwhile, everywhere else Sega just releases Sonic 3 with the original release soundtrack, until...
11) At some point, Brad Buxer decides to release unreleased tracks from his band "The Jetzons". Eventually, the Sonic fans researching Jackson's involvement come across this and listen to the track "Hard Times".
The similarities to Ice Cap Zone make the music go viral.
12) Meanwhile, Sonic 3 released on Steam.
13) tl;dr Brad Buxer's estate smells blood and there's implications of behind-the-scenes legal action.
14) Sega spends around the timeframe from 2012 to Sonic Origins' prerelease not acknowledging anything from Sonic 3.
15) Meanwhile, Sonic fans find a prototype of Sonic 3. Hoping to find more Jackson tracks, they instead find a build that has tracks like the ones in Sonic & Knuckles Collection, suggesting that these were the tracks the game was originally designed with after all. Why the Jackson tracks are in the final Sonic 3 when these tracks existed all along is now a mystery for the ages.
16) The tracks affected by all this; Knuckles theme (Sonic 3 version), Miniboss theme (Sonic 3 version), Carnival Night Zone, Ice Cap Zone, Launch Base Zone (both acts for all of these), Sonic 3 credits, Competition menu. Note that this is a select few (though notable) tracks, not the entirety of the game like is testified that has been done. If Jackson's sound team composed any further tracks, they are now lost media.
Gosh, I TRIED to make it short...
What have the replaced the music with?
It may not sound like this, but here are some tracks from the earlier-mentioned prototype for reference.