After Sonic had recovered the Chaos Emeralds following his first victory over Dr. Robotnik, he tried to find a safe place for them where they would be beyond anyone's reach. Before he could do that, however, the energy of the emeralds destabilized and the stones vanished in a flash of light, warping back to the Special Zone where Sonic had collected them. When the emeralds vanished, they released a burst of Chaos energy that struck Sonic and transformed him into an uncontrollable being of immeasurable power. This was the birth of Super Sonic, a violent, destructive alter-ego of the heroic Sonic. Before he could hurt anyone, however, Sonic took flight and catapulted himself across the planet Mobius, soon coming to crash in an uninhabited zone. He returned to normal quickly after, but would become Super Sonic many other times in the future.
Sonic's alter ego
For years, Sonic ran the risk of turning into Super Sonic when he became overly stressed (usually in unescapeable certain-death situations) or when he was exposed to high levels of Chaos energy. When transformed, Sonic became completely homicidal, flying into berserk rages and destroying any enemies he came across. Fortunately, most of these occasions involved Sonic being threatened by Robotnik's Badnik forces and so the robots would be the only casualities of Super Sonic's rampages.
Seperation from Sonic
In the three-part STC story "Running Wild", Sonic was accidentally exposed to enormous levels of Chaos radiation after falling into the well that held the Chaos Emeralds. After turning into Super Sonic, he decided to hunt down Amy Rose, one of Sonic's friends and fellow Freedom Fighters who had recently become a nuisance to Sonic. He finds the Freedom Fighters' caravan and moves in for the kill, colliding with the vehicle and destroying it. Knowing that they can't outrun Super Sonic, the FF trick him by remotely activating their biplane and allowing Super to shoot it down. Amy and the others go into hiding and Super Sonic cackles maniacally over the destruction he has wrought. As he laughs, he reverts back to his normal self and looks at the scene with an expression of horror, believing he had just murdered his friends.
After this incident, the guilt-ridden Sonic tries to keep a low profile in the slums of the Metropolis Zone. Unfortunately, he gets discovered in a bar and the locals try to capture him in order to claim the bounty that Dr. Robotnik has put on his head. Sonic warns his would-be captors not to make him angry, but for naught. He turns into Super Sonic again and tears the bar apart, sending the patrons running for their lives. When Super emerges from the establishment, he finds the Freedom Fighters outside waiting for him. He doesn't question how they are still alive and just tries to kill them again.
Tails tries to keep Super Sonic distracted whilst Amy Rose and Johnny Lightfoot set up a Star Post: a device that Sonic has previously used to travel to the Special Zone. They re-configure it to channel and drain the Chaos energy from Sonic, saving him from himself by removing that which causes him to become Super. The energy is drained from Sonic's body and deposited in the Special Zone, freeing Sonic from the demon once and for all. At least, that was what the FF had hoped for. As it turns out, Super Sonic is still alive and now exists as a seperate entity within the Special Zone.
While stuck in the warped dimension of the Special Zone, Super Sonic travelled to New Tek City on the planet Meridian, where he met the sinister crime-lord Lord Sidewinder. Believing that Sonic would eventually come for him, Super offered his services to Sidewinder if Sidewinder brought Sonic to him. Sure enough, Sonic arrived on Meridian with the help of the Chaotix Crew and Sidewinder arranged for the two hedgehogs to meet. With Sonic in his sights, Super immediately went back on his word and threatened to kill Sonic and Sidewinder's whole gang. His rampage was stopped when the Chaotix arrived with the Omni-Viewer, who sucked Super Sonic into his workspace and imprisoned him by freezing time inside its frame.
Though the Omni-Viewer had been immobilised trying to contain Super Sonic, Super was too powerful to be restrained indefinitely and the Omni-Viewer was only able to slow time to a crawl inside its workspace. Super Sonic was slowly pushing his way out, and so Sonic and the Chaotix decided to seal the Omni-Viewer inside the Black Asteroid, a barren, rocky planetoid. They left the Omni-Viewer at the asteroid's innermost cavern and then sealed it off, entombing it.
In the run-up to STC's 100th issue, Super Sonic managed to free himself from the Omni-Viewer only to find himself sealed within the Black Asteroid. The Omni-Viewer teleported to safety while Super remained trapped in the asteroid, but he would not be contained forever. The demonic hedgehog began building up tremendous levels of energy, superheating the Black Asteroid and making it appear to those on Meridian to be a second sun. Meridian's scientific elite determined that the asteroid would soon explode and that its explosion would generate an electromagnetic pulse that would blanket the whole planet, shutting down all electronic machinery.
After the Omni-Viewer had recharged, he informed Sonic of the situation. Sonic then suggested that the Omni-Viewer teleport the Black Asteroid to Mobius' orbit, since most of the electronic systems on the planet were under Robotnik's control and a worldwide EMP would surely cause his empire to collapse. The Omni-Viewer warped the asteroid to Mobius and then did the same for Sonic, who reunited with his Freedom Fighter friends and fought against the now-free Super Sonic. As fortune would have it, Super Sonic had used up so much energy by freeing himself from the Black Asteroid, his powers began to fail and he grew weaker. He fled the scene and the FF let him go since their priority at that moment was finding Robotnik and bringing him to justice.
After escaping the Black Asteroid, Super Sonic not only lost his powers but also his memory. He completely forgot who he was and was left to wander the streets of the Metropolis Zone alone for quite some time. He would eventually come to meet Ebony the Cat, a mystic who ran a coffee shop, and he asked her to give him a job. Ebony's psychic partner Pyjamas, however, did not trust this strange boy and feared he would only attract trouble. But Super Sonic was desperate for answers and Ebony was unwilling to turn him away, and so Pyjamas tried to establish a psychic link with Super Sonic in order to restore his memories. The link worked, much to Pyjamas' and Super's mutual horror. Super remembered who and what he was, but he had come to regard Ebony and Pyjamas as friends and feared that if he ever used his powers again, his demonic persona would regain control and endanger the whole world.
For years, Super Sonic lived happily with Ebony and helped her out around her coffee shop, all the while trying to keep a low profile since Sonic and the Freedom Fighters were still looking for him. Unfortunately for Super, the Chaos energy that sustained him was all but exhausted and he began to slowly wither and die. Both he and Ebony went in search of a source of power in order to save his life, and an opportunity arose when Dr. Robotnik had gathered the Chaos Emeralds in order to feed the monster known as Chaos. Ebony and Super Sonic joined the Freedom Fighters at Robotnik's fortress to battle against Chaos, and Super threw himself into Chaos' liquid body and absorbed the Chaos Emerald energy, restoring himself. Chaos, meanwhile, had been turned back into his original fish form and Super Sonic threw him into a nearby lake.
Sadly, Super Sonic's demonic personality reasserted itself after he had re-energised and he attacked Sonic and the others. In order to save the planet from Super Sonic's wrath, Ebony used her magic to reintegrate Sonic and Super Sonic into a single being again. This meant that Sonic would once again become Super when exposed to Chaos energy or when he became distressed.
Powers and abilities
Super Sonic possesses all of Sonic's abilities increased to a greater degree. As well as those abilities, he can also fly, fire energy beams from his eyes and create barriers. He is invulnerable and no conventional weapons or attacks can harm him.