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Whilst Doctor Eggman is still Sonic the Hedgehog's most enduring villain, he's not the biggest threat most of the time. Especially as Sonic's adventures have gotten bigger and grander, Eggman's plots more often than not involve getting/tricking other beings to fight Sonic for him, rather than coming into any direct conflict.
These schemes almost always go wrong, and whatever force Eggman was trying to control betrays him, leaving Sonic the Hedgehog to clean up the mess and save the day. This has led Sonic to face off against unbelievably powerful opponents, ranging from those with powers far beyond his own to literal Gods.
8 Silver The Hedgehog
A boss fight that lives in infamy amongst Sonic fans, as one of the most stupidly designed boss fights of all time. Silver is a powerful hedgehog, with strong Telekinetic powers, which can be used to great effect when he is a playable character.
As a boss fight, he's a horrible opponent who can kill a player instantly without any input from them. Silver's main attack is a burst where, if Sonic gets too close, he'll be caught and thrown by Silver's powers. However, Silver moves a lot during the fight, and if he catches the player against a wall, or above him, he will continuously do this attack with no way for the player to escape.
7 Shadow The Hedgehog
Shadow is arguably among Sonic's most powerful opponents, but he loses ground on the rest since he would eventually become an ally to Sonic during the events of Sonic Adventure 2, and even if he is still moody and grouchy whenever Sonic is around, he'll still help the blue blur save the day if he can.
The two hedgehogs battle a couple of times in Sonic Adventure 2, and depending on which story is being played, Shadow may win those fights. Outside that, he has extensive powers and control over the Chaos Emeralds that Sonic could only dream of.
6 Metal Sonic
Another opponent with very similar powers to Sonic himself, Metal Sonic has proved to be an enduring rival, starting as a tool for Eggman, but eventually becoming a villain in its own right. His powers are almost identical to Sonic's, but with a little extra spice.
As well as super-speed, he is made of a very tough metal, making him more resistant to damage. As a robot, he can use extensive weaponry and plasma attacks. Then, there's his form in Sonic Heroes, where he can shapeshift, and turn into the Metal Overlord, which required Super Sonic's power to beat.
5 The Nocturnus Clan
Stars of Bioware developed RPG on the Nintendo DS, The Nocturnus Clan are the last surviving clan of the Echidna race, other than Knuckles. They were ripped from the world in the Argus Event, where an interdimensional being looked to stop their power-hungry, warmongering ways by sealing them in a prison dimension known as the Twilight Cage.
In Sonic Chronicles: The Dark Brotherhood, they manage to escape the cage and display their superior technology. They have powerful weaponry and teleportation abilities, as well as robots beyond compare. Their leader, Imperator Ix, can even harness the power of the Master Emerald to achieve a super form similar to that of Super Sonic.
4 Perfect Chaos
A mutated Chao that is immortal and made of energy, it easily ranks among Sonic's greatest opponents. After being attacked by the Knuckles Clan in ancient times, Chaos was consumed with a fury that threatened to destroy the world, but it was eventually stopped by being sealed inside the Master Emerald.
Unleashed by Eggman during the events of Sonic Adventure, Chaos grew in power with every Chaos Emerald it absorbed, eventually betraying Eggman and absorbing all of them, to become Perfect Chaos. This being was as big as a city and could've easily wiped out the world in less than a day if Sonic hadn't stopped it.
3 Perfect Dark Gaia
The modern era of Sonic games went hog-wild when it came to lore additions, as Sonic Unleashed's big bad is an ancient God-like evil that was sealed in the world's core. Dark Gaia is prematurely awoken when Eggman broke the core of the world in half, but it was ok because it wasn't powerful enough to do anything.
Unfortunately, Eggman had to go and mess it up by retrieving the scattered fragments of Dark Gaia's power, allowing it to properly awaken and consume the entire world. This leaves Sonic to do what Sonic does best, take on a being with God-like powers and somehow come out victorious through bravery and force of will. He did at least have help from Light Gaia this time around.
2 Time Eater
Not content with just having an ancient God destroy the world, in Sonic Generations, Eggman harnessed the power of a being with dominion over time and space to try and erase the universe and start over. That goes about as well as it sounds.
Unlike most games, though, the power of two Eggmans (Eggmen?) allows them to retain control over the creature, forcing Sonic to team up with the classic version of himself. This creature's powers aren't entirely clear, but it could definitely destroy the universe if it wanted to, and it took the powers of two Super Sonics to take down. Not bad of a 15-year-old.
1 Solaris
It may feature in the worst Sonic game and plot of all time, and one that fans wish they could forget, but Solaris is undeniably the most powerful being Sonic has ever had to fight. Solaris is the combination of two other powerful beings, Iblis and Mephilis, who are tough cookies in their own rights.
When they combine, Solaris is formed, who is essentially the God of Sonic's universe, with the power to erase everything if it wants to, and it did want to. It took the combined powers of three super hedgehogs to take it down, and even then, Sonic, Shadow, and Silver had to very carefully coordinate their attacks to even hurt it.