Sonic races through the green fields. The sun races through a blue sky filled with white clouds. The ways of his heart are much like the sun. Sonic runs and rests; the sun rises and sets. Don't give up on the sun. Don't make the sun laugh at you.
— Words taken from Japanese cover of Sonic & Knuckles.
Sega's third 16-bit entry in the Sonic the Hedgehog series, and the followup to the wildly popular Sonic the Hedgehog 2, was so epic that time and hardware constraints forced them to split it into two separate games:Sonic the Hedgehog 3, released on February 2, 1994, covered the first half of the game, with gameplay as Sonic, Tails, or both. Knuckles the Echidna, the final member of Sonic and Tails' Power Trio, made his debut in this game, but as an antagonist rather than a playable character.Sonic & Knuckles, released on October 17 of that same year, covered the second half of the game, including Knuckles' Heel-Face Turn, and allowed gameplay as either title character (but not Tails).The game also featured "Lock-on Technology", a slot on top of the cartridge in which another Mega Drive / Genesis cartridge could be inserted. By connecting the Sonic 3 and Sonic & Knuckles cartridges this way, the two could be played as one complete story, Sonic 3 & Knuckles, with all three characters playable for the entirety, as was originally intended.When playing as Sonic or Tails, the plot picks up right where the Genesis Sonic 2 left off. Dr. Ivo "Eggman" Robotnik's Death Egg, just recently destroyed by Sonic, crash lands on the mysterious Angel Island (or Floating Island, as the American game manuals called it). Sonic and Tails follow, intending to stop Robotnik from rebuilding the Death Egg. Not one minute after landing, Sonic gets a face full of fist, courtesy of the island's native inhabitant: Knuckles, the last surviving Echidna and protector of the Master Emerald whose power keeps Angel Island aloft. Knuckles is convinced that Sonic is a thief who intends to steal said Emerald. Why? Because Robotnik told him.So while Sonic and Tails thwart Robotnik, Knuckles waylays them with traps and all around acts as a thorn in their side. This finally comes to a head when everyone reaches the Hidden Palace: Robotnik steals the Master Emerald and electrocutes Knuckles for trying to stop him. Knuckles realizes he's been had, and immediately joins Team Sonic, showing them how to get out of the Hidden Palace and onto the Death Egg.The plot of Knuckles' game covers most of the same levels as Sonic's, and features Knuckles fighting one of Robotnik's EggRobos (rather than the Doc himself) piloting souped-up versions of the level bosses. This culminates with a battle in the clouds against a Master Emerald-powered Mecha Sonic. It's a bit unclear when this all occurs in relation to the plot of Sonic's game. Official sources, such as the game manuals, imply that both plots occur simultaneously. However, in-game details appear to contradict this, and suggest that Knuckles' plot begins shortly after the end of Sonic's plot.The gameplay represented further Sequel Escalation compared to Sonic 2: The top speeds were even faster, the levels were even larger, and for the first time every Act featured a boss fight.note Although, if you play as Knuckles, you get to skip the Carnival Night and Lava Reef main bosses, and Hidden Palace is just an interstitial breather. There was more focus on plot as well—Knuckles' antagonism towards Sonic and Tails was shown through a number of in-level, wordless cut scenes, and every level ends with a brief scene of the characters traveling to the next level (the second act of each zone typically started exactly where the first act ended, with the player simply regaining control after the end-of-level sequence).A number of game mechanics made their Sonic debut here as well, such as a game save feature and specialized shields. The Special Stages from Sonic 2, where the Chaos Emeralds could be won, were revamped, and three different Bonus Stages were introduced, where extra rings and powerups could be collected. Cast Speciation (first introduced in the previous year's 8-bit title Sonic Chaos) was further developed: Sonic could make use of a brief, midair "Insta-Shield", and do a special attack while having one of the shields (a double-jump with the lightning shield, a bounce attack with the bubble shield, a fiery charge attack with the fire shield); Tails could fly (by himself or while carrying Sonic) and swim; and Knuckles could glide and climb sheer walls, but couldn't run as fast or jump as high as Sonic.Sonic & Knuckles' lock-on technology also worked with the Sonic the Hedgehog 2 cartridge, allowing you to play Knuckles in Sonic 2. The developers attempted to implement a similar feature with the original Sonic the Hedgehog, but found that Knuckles' color palette was incompatible with the game's (though a fan hack eventually proved that Knuckles could indeed be implemented in Sonic 1, by using two shades of red on his sprite as opposed to four or five). Instead, combining the two cartridges gives you the Blue Sphere minigame, with over 100 million variations on the Special Stage.Oddly enough for a franchise at its peak, this would be the last core series Sonic game until Sonic Adventure, which directly follows this one. Sonic the Hedgehog 4 is a proper sequel, though the Excuse Plot of Episode I doesn't suggest it.
And I Must Scream: Subverted: when you beat the Lava Reef Zone boss, Robotnik sinks into the lava, which cools and hardens seconds later. After the Knuckles fight in Hidden Palace Zone, he's shown to be perfectly fine.
Another Side, Another Story: ...Maybe. It's hard to tell, given the minimalist style of 16-bit era storytelling, but Knuckles' adventure might actually take place after Sonic's; see here for an analysis.
Artistic License - Physics: Granted, the game was never meant to be physically realistic, but one notable point is that the second phase of the Doomsday Zone's boss implies the presence of drag in space, given that the ship shoots bombs forward, that then slow down and fall behind.
Attack Drone: As Super Tails, the golden Flickies that follow him serves as such, immediately attacking any enemy or boss that's on-screen.
Berserk Button: The second stage of the Death Egg Zone's miniboss seems to have one: it will start spinning a pair of spiked platforms extremely rapidly while firing off a massive laser beam if you attack it.
Blackout Basement: Carnival Night Zone Act 2 (for Sonic and Tails), and Sandopolis Zone Act 2.
Bonus Stage: Unique among Sonic games for having two types:
"Special Stages:" A 3D maze where you must "Get Blue Spheres". Finishing earns you a Chaos Emerald. Accessible via giant rings hidden in the levels.
"Bonus Stages:" Stages for collecting rings and powerups. Accessible via a circle of stars that appear if you pass a star post with 20 or more rings.
Book Ends: The game begins with Sonic flying towards Angel Island by plane and ends with him leaving. By collecting all Emeralds, Sonic also brings the Master Emerald back to Knuckles, who had taken the Chaos Emeralds from him in the beginning.
Boss-Only Level: The Doomsday Zone. Technically applies to the Death Egg and Lava Reef bosses as well, if only by programming. Knuckles' version of Sky Sanctuary also qualifies, as it consists of his last two bosses and no platforming whatsoever.
Brick Joke: As you run through Launch Base Zone Act 1, you'll eventually find Dr. Robotnik carrying some sort of box around. That's the stage's midboss. When you defeat it, you might notice there are another two boxes in the wall. Those are the ones Knuckles will later fight in his version of the level.
Chekhov's Gun: The breakable objects that Knuckles could...er, break through to reveal alternate paths through the levels were this in the original Sonic 3, as the player could clearly see pathways behind some of them, but had no way to get there until Sonic and Knuckles was released.
The Archie comic had a short adaptation of Sonic 3 in issue #13, and also a 48-page special based on Sonic & Knuckles. Neither story actually featured the Death Egg (as that was saved for a later mini-series).
Sonic the Comic had Robotnik's second Death Egg being stuck on the Floating Island for the span of about 19 issues, the first four of which adapted the plot of Sonic 3, and the last five of which were based on the closing levels of Sonic & Knuckles.
Inverted in Hidden Palace Zone: Sonic can be airlifted by Tails to a hidden area where there are 30 extra rings. With those and the other rings that aren't hidden, Sonic can turn into Super/Hyper Sonic for the Knuckles battle.
Worse when Tails transforms, as any boss or enemy (except Knuckles) will get pecked to death by Tails' Super Flickies.
Continue Your Mission, Dammit!: See Idle Animation, but also, after Knuckles lowers the bridge for you in Sky Sanctuary Zone, ducking next to him makes him look at your character and wave his arm, as if telling you to go on without him.
And, in Sonic's continue screen, Tails tugs at his arm while pointing forwards.
Continuity Nod: Many details and changes in scenery make it clear that, messups aside, Knuckles' story takes place after Sonic defeats Dr. Eggman.
Convection Schmonvection: Two-thirds of Angel Island Zone is in the middle of a massive forest fire, yet the characters don't seem to mind. And naturally, Lava Reef Zone's lava only hurts you if you actually touch it.
Conveyor Belt-O-Doom: Death Egg Zone has elevators with conveyor belts that randomly switch direction and try to force Sonic into spikes or gun turrets.
Co-Op Multiplayer: As in the previous game, a second player can control Tails when playing as Sonic and Tails in single player, the difference being that Player 2 can now fly with Tails as well as pick up Sonic and carry him around. Versus mode is back as well.
The Determinator: Given how many mechs he goes through, Robotnik certainly comes off as this come the Death Egg and Doomsday Zones. He simply will not give up the Master Emerald no matter what.
Most of the environmental hazards of the game can be rendered harmless with the right shield. Lava Reef Zone is obviously best played with the flame shield, whereas the lightning shield becomes extremely useful for running safely on the electrified floors and ceilings of Death Egg Zone.
One subversion is that Knuckles fights Dr. Eggman instead of EggRobo in Flying Battery, breaking continuity due to not using or not being able to implement a unique sprite for EggRobo in that zone. There is a proper EggRobo boss for Knuckles in Carnival Night, should you make your way to the boss with him. Knuckles can also reach one of Sonic's routes in Lava Reef to find a stuck Death Egg in the background, which should be gone.
Difficult, But Awesome: The insta-shield of Sonic's. Slightly increases the range at which you can hurt enemies, and allows you to phase though things like projectiles, invincible enemies and other terrain hazards. It only lasts a split second though, so good timing is an absolute must.
Sonic gains extra maneuverability when he has a shield or is Hyper (he gets a double-jump in any direction). His insta-shield extends his hitbox, as well. As a result, Sonic is generally played more aggressively and recklessly.
Tails has a slightly smaller sprite, and can fly and swim. While flying, his tails become a hitbox. He cannot go Super with only the chaos emeralds, but with the super emeralds he gains homing attack Flickies. Tails is generally played more evasively, circumventing level hazards rather than blazing through them.
Knuckles can glide and climb, and has very poor jump height, which makes it necessary for him to punch through rock walls and access special level routes. Because of his poor jump and unfamiliar levels, and the slow initial speed of his gliding and climbing, Knuckles is usually played cautiously and tactically.
Dueling Player Characters: During the Hidden Palace Zone, Sonic finally gets to fight Knuckles, who had been hindering at every available opportunity after being told by series Big Bad Dr Robotnik that Sonic was in fact the villain of the two. The inverse doesn't happen, as Knuckles' story takes place after Sonic's & he needs to lose the fight to iniate his Heel-Face Turn.
Much of Knuckles' content is present in the Sonic 3 cartridge, but can't be accessed without attaching it to the Sonic & Knuckles cartridge. Also happens in reverse: in the combined game, when you play Launch Base Zone (the final level of Sonic 3) as Sonic or Tails, the game skips over the original final boss of the level (including the awesome ending music). Though you do still fight it if you play as Knuckles.
The standalone Sonic 3 cartridge has the Sonic & Knuckles miniboss music dummied out, you can hear it during the Hydrocity Zone Act 1 boss fight if you wait until the drowning music starts, then jump out of the water.
The standalone Sonic 3 cart also has Mushroom Hill, Flying Battery, and Sandopolis listed in its level select, none of which are accessible without locking onto Sonic & Knuckles.
Another reversed example: the infinite oxygen of the bubble shield is useless in the standalone Sonic & Knuckles, as it does not contain a single underwater section.
The Sonic & Knuckles music is also in the Sonic 3 cartridge. All of it. In the sound test, most of the Zone music that exists in track 09 onward is from Sonic & Knuckles. So its dummied out in that its not used but its still in the cartridge.
Evil Knockoff: Mecha Sonic. Ironically, in the first two fights, he uses Robotnik's tactics by reusing boss machines from previous games. In Knuckles's playthrough, he's The Man Behind the Man and final boss.
Faceship: The Death Egg, which has Robotnik's face on it.
Floating Continent: The setting of the game, although it got knocked out of the sky by the Death Egg's crash landing prior to Sonic's arrival. It gets raised at the end of Sonic's story path and remains afloat throughout Knuckles's until Mecha Sonic steals the Master Emerald.
Foreshadowing: When fighting against Knuckles, there is a background mural depicting Robotnik stealing the Master Emerald, and Super/Hyper Sonic attempting to stop him. Guess what you have to do in the true final level?
Fungus Humongous: Mushroom Hill Zone has mushrooms large enough to bounce on, use as a seesaw catapult, and parachute from.
If you kill the Marble Garden Act 1 boss off-screen by using co-op Tails, as soon as the goalpost lands, the game crashes.
Hyper Sonic is a virtual game breaking machine, since the developers more than likely didn't fully test him, given that he was a last second throw-in that is normally only usable at the end of both games. But start the game back up from the first Act, and you get enough bugs to fill up three hours worth of glitch videos on YouTube. Luckily for most players, many of these are almost impossible to trigger while playing normally.
Tails can also trigger several game breaking bugs (usually exploiting the fact that he doesn't clip with objects in the world if he is just off screen), but most of these also require the player to intentionally go out of their way.
On that note, some copies of standalone Sonic 3 have a real showstopper. Sometimes when you beat the boss of Hydrocity Act 2 as Tails, the screen remains locked in place and won't let you go over to the capsule, thus forcing the player to reset the game and play the entire level all over again.
The debug cheat allows for a variety of these. One common bug is to enter sprite placement mode while the player character is spinning. The graphics will glitch up momentarily, then the game will reset.
After the Angel Island Zone is set on fire, there isn't really any dramatic change to the gameplay to indicate that the Zone's on fire. No coming face-to-face with flaming walls or anything. It has basically no gameplay effect whatsoever, aside from one zip line that cuts off fairly quickly because a small section of it is burning halfway down.
Knuckles shuts off the lights in Carnival Night, but aside from raising the water level for all of 30 seconds, it seems to do nothing except show off how much of a prick he is.
Gotta Catch 'Em All: In Sonic 3, there are 7 Chaos Emeralds to collect, and getting all of them lets you use the first Super Mode (unless you're playing as Tails). Later, once you get to the Sonic & Knuckles levels, you can power up the gems into the Super Emeralds... and collect them again, for a total of 14 Emeralds. Getting the second set lets you use your character's hyper form (which then lets you use Tails' Super Mode).
Gravity Screw: Used extensively in Death Egg Zone, as well as the anti-gravity platforms in Carnival Night. Debug mode allows you to reverse the player character's gravity at will.
Guide Dang It: In what is probably the most famous example of all time, there is one point in Carnival Night Zone Act 2, where a red-and-white barrel (the Barrel of Doom) is blocking the path. The only way to proceed is by standing on the barrel and pressing up and down on the D-pad as the barrel wobbles. There's absolutely nothing in the game itself to suggest this.
It is possible to get past it with well-timed jumps (jumping on it is the only action that gives obvious feedback) and turbo spin-dashing under it as it recoils back up, but it is certainly not the intended solution and it's too easy to run out of time trying to pull it off.
Hand Wave: What the instruction manual does in regards to certain glitches, where Mercy Invincibility could cause you to get stuck in certain places and be forced to reset the console, handwaving them as one of the "many diabolical traps" set up by Robotnik.
Eggman's depth charges in the boss fight of Hydrocity are the means by which you launch up to hit him.
The mid-boss of Carnival Night Zone has a spinning disc with spikes on the edge. The disc is supposed to destroy the floor beneath your feet but if you hit the machine, it opens up and when the disc makes contact, will damage the machine.
The Act 1 boss at the Flying Battery can be beat by making it hit itself in the head by standing on top of it and running away really quickly.
The first Act 2 boss of Flying Battery causes the whole place to shudder and collapse by recklessly firing into the floor.
The mid-boss of Sandopolis will leap into a sand pit (hitting him does no good except throws him backward).
The boss of Lava Reef is destroyed when his mines slide into him.
The first boss of Death Egg Act 2 launches rolling spiked mines at you but if you reverse the gravity when the spikes are facing the machine launching them, they will damage it instead of you.
Hub Level: The area where the Master Emerald is kept becomes sort of a Hub Bonus Level when playing the second half of the linked game; entering a giant ring sends you there, where you can choose which Super Emerald you'll try to obtain.
Idle Animation: As in the previous games, Sonic will look at the player and tap his foot impatiently if the player does nothing for several seconds, occasionally pointing in the direction he's currently facing. A Dummied Out animation had him falling asleep as well.
Tails will stare at the player and occasionally yawn.
Infinite 1-Ups: Those alarm lights that trigger flying enemies in Launch Base Zone. Hold down a spin dash in one of those alarms, and a constant stream of enemies will fly right into you and be destroyed. The score given for the chain of hits eventually results in one life being granted every 3 secondsnote After you destroy 12 enemies, you get 10,000 points for each enemy destroyed; you get a one-up every 50,000 points., and even if you die by time out, since it's before the first checkpoint, you can just walk back there and do it again. There is a limit to how many lives can be recorded, and also a cap on your score.
Invisible Wall: Appears in a cutscene in Carnival Night Act 2, and just before the first boss battle in Launch Base Act 2.
Levels Take Flight: Flying Battery Zone features a few segments where the player must navigate the outside portions of Robotnik's ship.
Load-Bearing Boss: The gigantic Eggman mecha at the end of Death Egg Zone. Makes sense, since it not only contains the power source for the whole station, but is also so darn huge that crash landing into the superstructure would certainly do the trick.
Logo Joke: In Sonic 3, the Sega logo remains in place as a blue ball blazes towards the camera before revealing itself to be Sonic, followed by a white flash that leads into the title screen. In Sonic & Knuckles, the Sega logo remains as the background turns into Angel Island, splits apart as the Sonic and the Death Egg land on the ground below, and voila, title screen.
Long Song, Short Scene: Some of the music from the individual Sonic 3 gets Dummied Out if you're playing the two games in tandem, including the fantastic miniboss music.
If you are playing Sonic 3 by itself and do anything that makes the music temporarily change (gain invincibility and have it wear off, start drowning and then jump out of the water, etc.) during either Hydrocity Zone boss, the song will switch to the Sonic & Knuckles mid-boss music instead of going back to the Sonic 3 version. The tune otherwise doesn't appear in Sonic 3 at all.
Marathon Level: The stages, compared to previous games in the series, are exceptionally long, but both acts of Sandopolis Zone and Carnival Zone Act 2 definitely stand out. This was possibly done to make up for the small amount of levels after the game was split into two.
Good luck finishing Death Egg Zone Act 2 (where your time at the end of the stage carries over to the final stage) in under 10 minutes.
Launch Base Zone Act 2, when playing Sonic 3 alone. The main body of the level can be quick if you know your way around; otherwise you'll be forced into a massive detour. Then you have to fight three bosses, with a cut-scene in between that (unlike in the locked-on game) continues to run down the timer. Oh, and the last boss has an annoying phase in which he goes back and forth at the top of the screen, then the bottom; during this period you can't hit him. Like every other stage, your time limit for the entirety of this is 10 minutes. Good luck.
Magikarp Power: While Sonic and Knuckles unlock their Super Mode after getting 7 Emeralds, Tails doesn't unlock his until he collects all 14 Emeralds. However, his Super Tails abilities (particularly the four birds who will attack any enemies or bosses in Tails' vicinity) are even more of a Game Breaker than Hyper Sonic or Hyper Knuckles in that you can literally kill almost every boss just by standing in one spot (since you're invincible) and letting the birds kill the boss for you.
Minus World: As Hyper Sonic, you can glitch-dash through walls into areas normally only accessible by Knuckles. A Pandora's Box of further glitches can be triggered from here.
Mirror Boss: Knuckles, if you play as Sonic and/or Tails, though he's ridiculously easy to beat. He is pretty much the same Knuckles you can play as, with the additions of a punch attack and the ability to block by ducking. He even takes Collision Damage, though trying to walk into him will just get you punched. But you can stand in front of him and get Tails to walk into him from behind if playing as Sonic and Tails. Tails takes damage too, but he's invincible (in 2P mode). If Knuckles drops from a glide on your head, only he'll take collision damage.
Nintendo Hard: At first, Tails appears to be easier to play than Sonic because he has a lot of freedom of movement, including flying and free swimming in water, but fighting the Marble Garden boss with just Tails is immensely difficult because you can only safely hit Robotnik's ship from the underside with your spinning tails while avoiding the drill and the jet exhaust, and it's nearly impossible to recollect any lost rings.
The giant ceiling laser from Flying Battery Zone is a Call Back to Sonic 2's Wing Fortress Zone.
In Sky Sanctuary Zone, you fight a rehash of the wrecking-ball boss from Sonic 1's Green Hill Zone, and the boss with the spinning things from Sonic 2's Metropolis Zone.note Interestingly, the slight alterations of sprite proportions and game physics made both fights rather different from the originals. The Green Hill boss was originally a Warmup Boss; here he's rather harder to damage without hitting the wrecking ball on the rebound. The original Metropolis Zone boss could only be safely hit at one point in his attack pattern; here, the boss is significantly easier because he can also be damaged while he's at the top of the screen doing nothing — plus you have the Insta-Shield to pierce his shield.
Marble Garden's mid-boss uses a burrowing attack based on Mystic Cave's boss.
One Game for the Price of Two: If you don't have Sonic & Knuckles, you can't play as Knuckles or play half of the story's levels. If you don't have Sonic 3, you can't play as Tails (with or without Sonic), play the other half of the levels, or do the 2-player mode. And if you don't have both games, you can't use the Hyper Modes (and Super Tails).
Oxygenated Underwater Bubbles: Present throughout Hydrocity Zone, and can be released by bursting open underwater balloons in Carnival Night Zone Act 2. There's also water in Angel Island, and Act 2 of both Icecap and Launch Base, but you have to use Debug Mode to access the bubble for those levels, as they aren't already placed.
Poor Communication Kills: Hidden Palace Zone has a mural showing Robotnik with the Master Emerald in his hands, and Super/Hyper Sonic confronting him. Knuckles misinterpreted this as Robotnik trying to save the Master Emerald from Sonic, and thus treated Sonic and Tails as enemies.
Power Floats: Super Mecha Sonic. Both of Sonic's super forms also hover above the ground when they're at full speed.
Power-Up Letdown: Because there are no levels with water from Mushroom Hill onward, the Bubble Shield becomes this.
Scenery Porn: Beautiful pixel art, and impressive parallax scrolling on the backgrounds. There are a lot of little cosmetic details to the graphics that were in no way necessary to making the game and are clearly an example of Doing It for the Art.
Secret Bonus: Complete an act with the clock on 9:59 (one second before a Time Over) and you are awarded 100,000 points, enough for two extra lives. Not easy as it is at that time you must land the critical hit on whatever boss you're fighting.
Easiest with Knuckles in Carnival Night Act 2, as he doesn't fight a boss. Just stand in front of the capsule until 9:58 or so and then jump and break the capsule. Requires patience.
Secret Level / True Final Boss: The Doomsday Zone, which is only accessible if you beat Death Egg Zone as Sonic, with a full set of Emeralds, and is just an extended fight with Robotnik's final Egg-Mecha.
Segmented Serpent: Flying enemies in Angel Island Zone, flying enemies in Mushroom Hill Zone, sand worms in Sandopolis Zone, and yet more flying enemies in Lava Reef Zone. Hitting them anywhere besides the head will injure you.
Spiritual Successor: Flying Battery Zone to Wing Fortress Zone from Sonic 2. Carnival Night Zone would appear to be this to Casino Night Zone from the name, but besides being brash and colourful levels they don't share much in detail.
Stalactite Spite: The stalactites and icicles in Lava Reef Zone and Ice Cap Zone, respectively.
Stalked by the Bell: In Sandopolis Zone Act 2, ghosts start to appear as lights in the level go out, and will start attacking unless the player continues to switch new lights on.
The Stinger: Like in the first game (and the 2013 remake of the second game), after the credits roll a small scene plays.
In vanilla Sonic 3, failure to collect all Chaos Emeralds shows Dr. Robotnik and Knuckles in possession of them, laughing. Likewise, failure in Sonic & Knuckles or the full game has either Dr. Robotnik or Mecha Sonic claiming the Master Emerald.
Collecting all Chaos Emeralds as Sonic or Tails in Sonic & Knuckles but not starting the Super Emeralds quest in the full game shows the last EggRobo awakening, which links Sonic and Knuckles' stories.
Story-Driven Invulnerability: At several points, Robotnik shows up outside of a boss fight but cannot be destroyed.note at least, not without exploiting some game breaking bugs that allow you to land 256 hits on him. The most notable instance is during his theft of the Master Emerald.
Bestowed by a Bubble Shield. Fridge Logic dictates that gas exchange between the water and the giant air bubble would not be able to keep up with Sonic's respiration, so Sonic would still run out of air, but who cares?
The Hyper forms of Sonic and Knuckles can breathe underwater without the bubble shield, but by the time it becomes possible to get these forms, you've already passed the last level with water in it. Breathing underwater is thus only relevant if you're replaying any of the zones with water on a save file.
Super Mode: In addition to the usual Super Sonic, it's also possible to play as Super Knuckles. And if you collect all 14 Emeralds you can become Hyper Sonic, Hyper Knuckles, or Super Tails.
Tactical Suicide Boss: Hot Mobile in Lava Reef Zone. The spikeballs it sends out eventually come back down the slope and hit itself. It's otherwise completely immune to Sonic's/Tails'/Knuckles' attacks (includingSuper/Hyper forms).
Threatening Shark: Inverted. The "Jawz" mook you face in Hydrocity Zone is arguably the easiest enemy to beat in the entire Zone. It slowly propels itself horizontally from offscreen, and while it has a tendency to appear suddenly and in groups, it can be hit anywhere with a spin attack or jump attack. The inversion is that Jawz appears exclusively in Act 2, while the much more bothersome Buggernaut appears exclusively in the Act 1. Hence, Hydrocity is actually better with sharks.
When playing as Sonic with Tails tagging along, it's possible to glitch Tails off-screen so he doesn't return. Doing so in Marble Garden Zone makes it impossible to fight the boss.
Also, in Hydrocity Zone Act 2, it's fairly easy (though fixed in the locked-on game) to go past the boss and right to the capsule without doing the boss fight. Unfortunately, for some reason, this prevents the level transition cutscene from playing, and while the timer keeps ticking up, you won't die when it hits 10 minutes. The only way out is to reset.
Urban Legend of Zelda: Despite what your third grade friends (and basic logic) told you, it's not possible to beat the Fire Breath the first time you see it and stop it from burning Angel Island. No matter how fast you hit it, it'll successfully set off the firebombs and escape with its robotic life.
Weaksauce Weakness: Fire shields let you run over molten magma and lightning shields make you a ring magnet and immune to electricity, but both are immediately cancelled if you touch water. Annoying in the Sonic 3 portion, with water in 5 of its 6 zones, but not once you reach the Sonic & Knuckles levels which have no water sections at all.
What the Hell, Player?: In Competition mode, if one player jumps the starting line before the countdown reaches "GO!", a buzzer plays, "FAULT" appears on their side of the screen, and the round restarts.
Wrap Around: A few areas in Ice Cap Zone and Sandopolis Zone tend to loop when not exited from them properly. With the Hyper Sonic in Sonic 3 cheat, you can wrap around back to the first act of a Zone, resulting in messed-up graphics and other glitches.