Robotnik's Evil Plan involving the Drakon Empire, resulting in him absorbing the power of the Chaos Emeralds, ruling over Mobius for eternity, and being capable of tormenting Sonic in any way he could think of.
Sonic's defeat of Robotnik here counts too, as it's one of the few times that he used his brain to defeat Robotnik, simply by appealing to his vanity and new found god-hood by pointing out that if Robotnik was so powerful, it wouldn't matter if Sonic had an ally or not, Robotnik would still win. Robotnik buys into it, and was manipulated into restoring Knuckles to normal, allowing the echidna to use his knowledge of the Chaos Emeralds to drain Robotnik's power using the Grey Chaos Emerald (the "control" emerald of the other six).
Before that, Sonic refusing to yield to Robotnik's attempts to break him via completely reshaping reality multiple times, citing that no matter what reality he's in, he'll always beat Robotnik, provoking Robotnik into restoring Sonic's powers just to show he's not afraid.
The Reveal of Robotnik having become a god with the power of the Chaos Emeralds - after his crystalline form seemingly shatters, the heroes hear his laughter echoing around the chamber, and run outside... where a giant Robotnik is holding the entire Floating Island in his hands.
The earlier reveal of him being alive in his crystal state.
Tails: Sonic, I- urrrk!
Sonic: Quit mumbling, Tails! If you want to say something, speak up!
Robotnik: *Holding Tails by the throat* Your little friend can't seem to get his words out, Sonic... I think there's something wrong with his neck!
Sonic:Robotnik?
Robotnik: *Throwing Tails to the floor* Thought you'd seen the last of me, didn't you, hedgehog?
Sonic: I should have smashed you while I had the chance!
Robotnik: Ah, but you didn't... and now it's too late!Much too late! I don't need Grimer any more... I don't need any Badniks or Troopers or help from the Drakon Empire...I am the force now!
One particular moment of the fight against the god-level Robotnik stands out; after Robotnik has recreated five of Sonic's most powerful foes- Metallix, Megatox, Plasma (and Arnem Abacus), Commander Brutus and Metamorphia- to fight Sonic at once, he mockingly observes that Sonic may have beaten all these foes in the past, but he never had to face them at the same time. Despite these odds, Sonic takes advantage of the situation by throwing Brutus into Plasma, the collision destroying the seemingly indestructible Brutus and causing a chain reaction that destroys all of the other villains at once.
The reason they defeated Robotnik to liberate Mobius counts here too, as the Omni-Viewer states that Super Sonic will cause a planet-wide EMP when he explodes the asteroid he was trapped in. Sonic immediately asks the Omni-Viewer if he can move the asteroid above Mobius, and when asked why, he simply smirks and says "Because most of the technology on Mobius is Dr Robotnik's!"
How does Sonic defeat King Sonic when he and Amy stumble into his world, where he is essentially Sonic crossed with Robotnik? Trick him into turning into Super Sonic - since this Sonic is evil and violent, it stands to reason his Super form would be calm and a pacifist. He's right.
Robotnik doing the one thing Sonic couldn't do: defeat Commander Brutus, a Robot with a copy of Robotnik's mind and made of the strongest metal on Mobius which even Sonic could not damage (though Super Sonic could - he ripped Brutus's arm off the first time they crossed swords).
Knuckles destroying Carnival Night Zone with one punch. He did this by punching the fault line near the Zone with one punch. Since the Carnival Night Zone was built on the edge of the Zone, Knuckles completely smashed off that portion of the Floating Island, removing Carnival Night from the island. A few seconds later, the Zone fell to Mobius, slightly cushioned by remaining Master Emerald power. The crash-landing of the ruined Zone was a shock to one Emerald Hill boy who had just before wished that the Zone was closer.
Knuckles helping Sonic to stop the Death Egg II by using the Floating Island and the remaining six Chaos Emeralds (Robotnik has the Green Chaos Emerald which is the Master Emerald) to power the ancient technologies installed throughout the island. With the island effectively turned into a flying fortress itself, Knuckles steered his home toward the Death Egg, unleashing a barrage of energy blasts that tore through the vessel's armored hull, destroying the Death Egg II.
Amy firing an arrow from a moving plane at a tiny little button that destroys an entire bridge.
Tails managing to successfully manipulate Super Sonic into stopping a volcano from destroying the Hill Top Zone by using reverse psychology and triggering Super Sonic's need to prove how powerful he is.
In Super Sonic's debut, Tails manages to talk Super Sonic down long enough for him to depower back to being Sonic.
Ebony and Pyjamas successfully stopping Super Sonic from lapsing into his psychotic ways and going on a rampage in Return of the Nightmare by trapping him in a fantasy and erasing his memory of having snapped.
After that, Ebony successfully tricking Sonic into thinking his energy tracker was displaying a false positive match for Super.
Robotnik successfully luring both Chaos and the heroes to his hideout just to see what the end of the world will look like.
The heroes successfully tricking Super Sonic into thinking he's succeeded in killing them with the bi-plane on remote control.
Later, their sudden reappearance surprises Super Sonic enough to distract him from his latest rampage to demand answers on how they survived their certain doom. This gives Amy an opportunity to distract him further while the team gets ready to depower him via Star Post.
Fighting Robotnik's final Doomsday mecha on the Floating Island during Disaster!, the finale to the Sonic & Knuckles adaptation, Sonic starts moving so incredibly quickly he rips the machine to shreds before unintentionally sending it toppling over the edge.
Sonic: Don't bother thinking of a reply, walrus chops... you don't have time!
Robotnik: First I'm going to squash you like the insect you are! Then I'm going to take care of your precious Emerald Hill Zone... permanently!
Sonic: You talk too much!
Robotnik: I... I've never seen him like this before... never so savage!The island's edge!Aaaaagh!
Robotnik: I tried going easy on those Emerald Hill worms! I tried to be a just ruler! But that's all over now! From now on it's NO MORE MISTER NICENIK!
Sonic and Knuckles' first encounter. Duped by Robotnik into thinking Sonic is after his Chaos Emeralds, Knuckles lays two hard punches to Sonic before the latter can explain anything. Sonic then reasons he gets it, Robotnik has just tricked the guy. But nobody hits Sonic the Hedgehog like that and gets away with it, and gives Knuckles a running Megaton Punch in return. Cue to the brawl.
Sonic defeats an invincible monster about to obliterate the Emerald Hill Zone by activating the monitor trap that had caused it to swap places with Tails right as it unleashes it's attack, freeing the fox and obliterating it's home of the hellish Misery Zone instead.
Faced with Megatox, a borderline intangible foe made of a liquid designed specifically to kill him, Sonic weaponises his speed to force Megatox down a pipe leaving the Chemical Plant Zone and scattering him across the countryside. It takes the creature so long to pull himself together that by the time he's a threat again, Sonic has completely forgotten he existed.
