WMG / Sonic 3 & Knuckles

Sonic & Knuckles is an unauthorized sequel.

Allegedly, Sonic 3 was concieved as a standalone game, but far up north, two midgets somehow programmed a flawless imitation of Sonic's game engine and used it to create Sonic & Knuckles. They tried to pitch it to their boss, who thought it would never catch on. Fortunately, these two guys successfully sold the idea to Sega, and got rich off of it, despite Sonic Team taking credit for the game. A rare mini-documentary talking about it can be found here.

Amy could have been playable in these titles

She was meant to be playable in Sonic CD

Sonic's modern look and powers are side effects of turning Hyper Sonic.

As Hyper Sonic, his eyes turned green, just like his modern look. Sonic 4, taking place after this, is the first canon appearance of the modern look and the homing attack. The biggest evidence is that as Hyper Sonic, he could unleash a double jump attack the propelled him further and destroyed any minor enemies on screen, and with the general ability to direct his momentum, and now the boosting he's clearly growing in power.

• As an add-on, exposure to Chaos energy is probably what turned his eyes green. The height could be explained by puberty.
• This also explains Eggman's growth spurt between this game and Sonic 4, despite being an adult. In Doomsday Zone, you ram his final robot to destroy it and win the game. Eggman somehow absorbed some of Sonic's energy from the hits, causing him to grow.

The asteroids in the Doomsday Zone are chunks of earth and pieces of the Sky Sanctuary that the Death Egg kicked up during its ascent.

How else does one explain asteroids in orbit above the earth?

In the Special Stages everytime you do the Orb Turns Into Rings thing someone is getting hit and losing rings.

Exactly what it says on the tin

Robotnik/Eggman himself designed the games and sets himself up for you to beat him

I've read that Robotnik/Eggman has an I.Q. of 300, and while still prone to mistakes or oversights, it seems odd to me that Sonic can defeat him relatively easy. This puzzled me as it's fairly obvious that he knows Sonic's weaknesses. He knows that Sonic can drown/be poisoned (Chemical plant). He knows that Sonic needs rings (Death egg zone in Sonic 2) and he even knows about the 10 minute clock (Death Egg Zone 2 in Sonic and Knuckles, a lot of the transport hoops take a long complicated path that does nothing but waste time)

So if he really wants Sonic dead, why not just set up a boss room that floods with poisonous chemicals, with no way out? Or trap him in a room for 10 minutes? Or have him fall into a boss room with an all spiky floor, that he can't jump out of, sort of like a certain pit in the Mystic Cave zone? Gameplay and story segregation aside, I think it's because Robotnik/Eggman knows that if he wins, things will get very boring very fast. A man with an I.Q. of 300 is likely a man who gets bored easily, and so when Sonic came along, someone who actually presented a challenge, he set things up to play a game with the blue hedgehog, complete with powerups of his own design (item boxes, shields, maybe even the rings themselves), and enemies, then waits and sees how well Sonic fares. Then he fights Sonic himself in a machine that has a built in weakness, and it's up to Sonic to exploit it.

Why else are the item boxes, which are clearly technology, there? It's even more obvious when you run across item boxes with Eggman's face on them, and opening those hurts you. Or the betting machines in the Casino night zone, or the fact that even Robotnik/Eggman's bases are pretty hedgehog friendly, what with Sonic sized tubes, and devices that Sonic can operate, or if you take Sonic CD into account, the fact that all the bad future levels are run down, even Robotnik/Eggman's bases. Without you, he no longer has a reason to keep them in good condition.

Hyper Sonic isn't canon.

• In Sonic 3 and Knuckles, the ending where Sonic beats Eggman using his Super Sonic form instead of his Hyper Sonic one shows a Stinger where a singular EggRobo stands on top of a pile of his broken comrads with the implication that this is the exact same EggRobo Knuckles faces in his story. Since it's implied in-story that the playable Knuckles' story takes place after Sonic's, this means that canonically Sonic never once, turned into Hyper Sonic even in this game.
  • Or maybe Knuckles' story is the non-canon one.

Knuckles was made as an Anti-Climax Boss on purpose

• Think about it: unlike Eggman he doesn't have any vehicles or technology and just fights you barehanded. Also, every time he got the drop on Sonic before he had the element of surprise or Sonic was unable to attack back effectively for whatever reason. Sonic totally kicking his ass is just a case of Surprisingly Realistic Outcome.

The Super Emeralds only existed because of the Master Emerald.

• The developers have gone on record as saying that the Super Emeralds are gone - "I don't know how, but they're gone." You only gain access to the Hyper Emeralds when you collect all 7 Chaos Emeralds to begin with, and enter a ring to Hidden Palace Zone, where the Master Emerald (currently) resides. The Master Emerald then granted power to the Chaos Emeralds due to proximity. After Sonic defeats Eggman in Doomsday Zone, proximity to the Master Emerald again removes the power from the Chaos Emeralds, leaving only enough energy for Sonic to make it to Earth and flash off a Hyper Form at the end of the credits. Knuckles can control this power of the Master Emerald, which is why he was able to knock away the Chaos Emeralds from Sonic in the first place, and later uses it in Sonic Adventure 2 during the Last Story. However, Knuckles is conveniently missing from Hidden Palace Zone every time Sonic visits it from a special stage ring, and thus the Master Emerald's power runs free and grants said power to the Super Emeralds. Every other time the Chaos Emeralds and the Master Emerald appear together in the series, Knuckles is around to keep the Master Emerald's power contained.

Knuckles would've been a Secret Character had the game been released as a single cartridge

• Imagine how cool it would be to see Knuckles constantly be your opponent without any idea he'd be playable only to end up unlocking him. I'd imagine his unlock criteria would be beating the game with all 7 Chaos Emeralds (the Super Emeralds were only created when the game was split in two). The reason for this rather than simply beating the game is that Master Emerald is never retrieved in the non-emerald ending. Furthermore, Knuckles' story clearly takes place after the good ending of Sonic/Tails' campaign despite what Sega claimed around the release of Sonic the Hedgehog 4, as such it would make sense to not have this mode available from the start. But once the game was split into two, Lock-On Technology became the selling point of the second half and they couldn't hide Knuckles' playability.