Sonic & Knuckles Collection presents the Sonic 3 duology on one disc, allowing players to choose to play the games separately as they were originally presented in cartridge form, or together as they were applicable via the Genesis original's "lock-on" technology. The games themselves are slightly modified; all of the games' music was converted to MIDI format, with options to play the soundtrack in either General or FM MIDI modes. Several Sonic 3 stages' music was completely replaced with MIDI versions of music from a Sonic 3 prototype. These are the ones that are, based on other evidence factors, theorized to be the ones originally composed by Michael Jackson and/or Brad Buxter.
The Sonic & Knuckles level select code also works in Sonic 3 alone/ by inputting it in Angel Island Zone. This allows players to utilize characters in stages ordinarily inaccessible to them. The titles, however, lack a debug mode.
Included on this CD-ROM are: