Sonic is continuing his journey across the Floating Island. He has just downed Doctor Robotnik's relaunching Death Egg, but it is still functional and could be launched again at any time. Sonic is also attempting to convince guardian Knuckles that he isn't after his Chaos Emeralds. Soon, all becomes clear when Robotnik betrays Knuckles and steals the Master Emerald. Knuckles stops harassing Sonic and leads him to the Sky Sanctuary Zone where Sonic boards the Death Egg and completely destroys it, before retrieving the Emerald.
- Mushroom Hill Zone - a leafy area filled with giant, bouncy mushrooms. Thanks to a device built by Robotnik, the seasons in this Zone have been known to change in a matter of seconds.
- Flying Battery Zone - an airship owned by Robotnik and piloted by an EggRobo.
- Sandopolis Zone - a desertous region that contains the Lost Pyramid of Sandopolis. Inside that are evil Sandopolis Ghosts eager to fend off all intruders.
- Lava Reef Zone - a volcanic area that substantially cools down later. It is reactivated when the Death Egg, resting on top of the mountain, fires its weapon.
- Hidden Palace Zone - home of the Chaos Emeralds.
- Sky Sanctuary Zone - a sacred echidna site somewhere above the Floating Island, it falls apart without any Emerald power.
- Death Egg Zone - Robotnik's ultimate spaceship.
- Doomsday Zone - a final dash through space as Super Sonic to retrieve the Master Emerald.
As Knuckles, the character can only play through the first six levels. As Sonic, you must have all 7 Chaos Emeralds to enter the final Zone.
Continuing Sonic 3's theme, Sonic & Knuckles introduces several new Badniks in each Zone. The following are ones that appear somewhere in Sonic the Comic:
An extremely faithful Sonic & Knuckles adaptation appeared in Sonic the Comic, making up the second half of the Sonic 3 & Knuckles story arc. With Robotnik continuing repairs on the Death Egg, Sonic eventually returned to the Floating Island to shut things down, beginning on the Sandopolis Zone. Unfortunately, he became sidetracked with the sudden appearance of Captain Plunder, who wished to rob the Lost Pyramid for his own gains. Aided by Knuckles and the Sandopolis ghosts, Plunder was soon defeated. The heroes moved on to the Lava Reef Zone, Knuckles disposing of a horde of EggRobos simply by punching a platform of lava into them.
Their adventure took them into the Emerald Chamber, where they discovered that the Master Emerald had been stolen by the Metallix Mark 2. The heroes gave chase to the Sky Sanctuary, where a super-powered Metallix easily beat Knuckles and pummeled Sonic. The tides turned, however, when Sonic became Super Sonic and quickly tore apart the threat (and almost Knuckles). He came to his senses in time to see the the Zone falling apart without any Emerald power. Gliding down on Knuckles' back, Sonic infiltrated the repaired Death Egg using the attacking Badniks as stepping stones, while Knuckles returned home to find a solution.
On board the battleship, Sonic was captured by more Badniks and taken to the control room. When the vehicle was attacked by the Floating Island, Sonic stole the Master Emerald but found himself plummeting down to Mobius. He was saved when he stole an EggRobo's jetpack, allowing him to fly over to the island. Although his Death Egg was finished, Robotnik attempted to have his way with Sonic one last time, but was accidentally punched from the island in his mech by Sonic, the dictator falling slowly back to Mobius. With the Master Emerald put back in place, Knuckles repayed Sonic's heroics by allowing the fugitive Emerald Hill folk to stay in the Mushroom Hill Zone.
Although the adaptation finished here, prominent parts of the game continued to feature through STC's run. The most important addition was that of Knuckles the Echidna becoming a hero as well as the varied landscape of the Floating Island. The Mushroom Hill continued to appear while the Emerald Hill folk lived there, but the only frequently appearing location from the game now is the Hidden Palace Zone.
Sonic & Knuckles (and combined game Sonic 3 & Knuckles) often tops reader polls on which Sonic game is the best, frequently beating similar favourite Sonic the Hedgehog 2.
David Gibbon covered the game twice in his Review Zone articles. He initially awarded the title 91% for being the best game yet and being compatible with the others, his only "grave" being that its longevity and lack of save feature could lead to "a few dinners going cold". Its re-release shortly before Issue 83 saw Gibbon repeat his "cold dinners" gripe, but this time only afforded the title 87%, notably awarding less than the re-release of Sonic 2 (91%).