Sonic & Knuckles levels are intended to pick up right from where Sonic 3's left off, and there is little difference in their brilliance, as they're both designed with the same ethos. The huge (perhaps even bigger) stages are rife with non-linear paths that branch out into sub-routes and secret areas, all of which could never legitimately be covered in one sitting. As with Sonic 3, two acts of one zone don't just stay the same but evolve in every aspect, be it the beautifully crafted scenery, the excellent background music, the structural features and the inventive objects and enemies you encounter. Though the majority of the levels are available to both, the two characters frequently indulge in their own exclusive routes on numerous occasions, thanks to their specific abilities, such as Sonic's higher jump or Knuckles' ability to more easily knock down barricades. As a rule, the challenges and bosses that Knuckles faces are just that little bit tougher.

Technically there are seven levels to explore, though unlike most titles in the series, their lengths and contents can vary dramatically as the latter half of the game begins to introduce more story-focused scenes into the levels than ever before. Like all of those in Sonic 3, the first four are divided into two large acts, each with a boss at the end of them. The first act boss will usually be a large robotic henchman of Eggman's, while Sonic will battle Doctor Eggman himself at the end of the second act. Knuckles meanwhile usually tackles an Eggrobo badnik, taking Eggman's place. The fifth and sixth zones however feature only one act apiece, in which the rule book is thrown out entirely. Hidden Palace Zone for Sonic is used purely as a scene in which the plot of the game takes a dramatic turn, and for Knuckles it's bizarrely no more than a very short walk indeed. The single act of Sky Sanctuary Zone throws a series of boss battles at Sonic amidst a vertically progressing level, whereas for Knuckles this acts only as the stage for his final battle. Only Sonic has access to the last, full two act level in which he boards the Death Egg once again. If he collects all seven Chaos Emeralds along the way, there is also one last, epic boss battle to encounter that can only be played as Super Sonic, thus kick starting an extremely common trend in later Sonic titles. So although Knuckles' levels are a tad harder, his overall game is cut short by quite a bit.