- Dr. Finitevus was once a fellow scientist of a race of prosperous echidnas, until a freak accident changed his looks and intelligence. Despite his new-found genius, he was declared mentally unstable and was to be put down. He escaped and later sold out his home to Dr. Robotnik. Everyone who had once lived there died later. Furthermore, this guy manipulated four whole sides in a war (Dingoes, Echidnas, and two Dark Legion factions) into providing the fuel for the fire of his master plan, which is him deciding the world is hopelessly corrupt and he wants to purify it...in fire. He, to this end, manipulated Dimitri, a head in a jar, into providing secrets and information, and then manipulated Knux into becoming Knuxerjak and starting a battle with his former friends after the whole corruption from power thing. Finitevus' expression at the scene where Knux becomes Enerjak shows he is not only mad, but completely delighted, even as his betrayed allies watch on and denounce him.
- The original Dr. Robotnik. During the Great War, he intended to test weapons he'd developed for the government on his own people and fled to the Mobian's side when he was to be punished for his actions. While acting as Warlord for King Acorn, he secretly captured a peaceful village of Mobian monkeys and utilized them in an early attempt to create mechanical slaves by surgically implanting cybernetics, and of that entire village only one survived the process. Afterwards, he sabotaged the roboticizer developed by Charles Hedgehog just as it was to be used on his wounded brother Jules, making him think he'd turned his own brother into a mindless drone. When Jules' wife discovered the truth, Robotnik had Jules toss her into the Roboticizer and transformed into a robian as well, orphaning Sonic and crushing Charles' spirit to the point of retiring from being a Science Minister to running a chilidog stand. He then did similarly to Tails' father Amadeus on the day of his birth, making it seem as though Amadeus could care less for his newborn son and subsequently shattering his wife's heart, throughout which Robotnik maintained a straight face. Afterwards followed his betrayal of King Acorn and the takeover of Mobius, during which countless families were broken and millions enslaved, and over the course of a decade, he'd wreak havoc upon planet Mobius, destroying the ecology and pushing more than a few mobian breeds to the brink of extinction. And just prior to his death, he displayed a deeply disturbing relish at the thought of murdering one of his own kind and was positively gleeful when he got the chance to use his latest and greatest weapon on a fellow overlander.
- Dark Enerjak is the tyrannical ruler of another dimension. He is actually a version of Knuckles the Echidna whose Chaos Powers went out of control, also fueled by a desire to make the world a better place. While he started out noble, he gradually went more and more insane as time went on, before he considered everyone an enemy. Among his atrocities are the sinking of a continent, the destruction of several enemy cities, such as Station Square, as punishment for their defiance, and the capture of his strongest opponents and ripping their souls out - victims including Sonic, Shadow, Tails, Amy, Sally, and all the villains, including the previously-mentioned Eggman and Finitevus. To re-affirm his evil, you get a full shot of many of his more prominent victims after he demonstrates the process on his newest captive. He turns the souls into robotic slaves known as "Prelates" with his power. His soulmate was one of his victims, and he made sure not to use her soul to form a Prelate until the final battle... he summoned her to fight their daughter, much to said daughter's disbelief. Dark Enerjak's mainly motivated by his own amusement, despite saying how much of a hero he is at other times. He allowed the Freedom Fighters to exist to give him something to do, sent soldiers to other dimensions to try and find new worlds to conquer, and continued to indulge Silver because of his power to actually give the living God a challenge. He derives joy from people's suffering, as seen with how he forces his own daughter to fight her mother and his former mate and how, upon seeing how upset Silver is at Enerjak using the souls to make his Prelate Army, he summons them all at once.
- General Kage Von Stryker is the leader of the Eggman-backed Dingo Regime. After ousting his father from power, Kage led his people in conquering Angel Island, imprisoning the Echidnas in what were clearly concentration camps, which led to countless deaths. He personally tortured Knuckles's father for the location of the Master Emerald, tried to wipe out the last echidna village on two occasions, and during the second attack boasted that he had crushed more Echidnas under his boot than he could remember.
- Hunter, as his name would indicate, would hunt down certain specimens of Mobian, and he debuted trying to do just this to Knuckles. Hunter revealed that not only did he hunt down Mobians, but that he would also claim their heads as trophies in the same manner of a real life hunter. After being defeated he would go on to work for Eggman and would become a gleeful participant in the genocide of the Echidna and other Angel Island inhabitants, capturing droves of poor souls to be sent to the Egg Grape Chambers, where they would perish in a slow, horrible fashion by having the very life drained of them. Though only a minor villain in the long run, his actions put him well beyond the point of redemption and into the realm of the truly malevolent, despite some pretensions earlier about having nobler characteristics.
- Shadow the Hedgehog: Big Bad Black Doom, the sinister leader of the Black Arms, essentially tried to torture every living thing on the Earth by paralyzing them with nerve gas from the Black Comet. After everything had been paralyzed, he and his offspring could then come in, and devour everything on Earth. This also included Shadow, who is who is Black Doom's biological son note . Even Dr. Robotnik himself is also disgusted by him.
- Sonic the Hedgehog (2006): Mephiles wanted to try and essentially eliminate Time itself, as well as the fact that he killed Sonic the Hedgehog for little reason than to make Elise cry so he could merge with Iblis and thus destroy time itself. Although Sonic got better, it's still quite the Moral Event Horizon. Its also implied that he was part of the reason why Shadow ended up sealed away by humanity as well as an unwilling Omega carrying out the deed (he had some resemblance to Shadow thanks to absorbing his shadow, so its not unreasonable that he would have done deeds that the populace will blame Shadow with), and he manipulated Silver into attempting to kill Sonic with the implied intention of destroying the past. If that's not enough, he also enjoyed the carnage he inflicted. He currently ranks highest in regards to being the most evil character in the series not only because of his motives simply being to wreck and destroy anything and everything he can for no reason other than For the Evulz at best, but also at how frighteningly close he came to succeeding in his goal to destroy everything, heavily damaging the time-space continuum.
- Big Bad Dr. Robotnik, unlike the version of him you'd see in other Sonic cartoons (or the games themselves), is much less pleasant. He is willing to deprive innocent creatures of their free will to get them to work for him, he is willing to turn formerly beautiful communities into severely polluted wastelands, and he doesn't show any remorse for any of his actions. He turns people into his robotic slaves if they don't obey him; they are quite aware of what's happening to them, and morally object to that which their robot bodies are forcing them to do. There are episodes in which some robots are carrying on secret conversations with their loved ones, from before roboticization, only to double over in apparent pain before proceeding to attack said loved ones because of the control Robotnik has over them. He even turns the ones who do obey him into robotic slaves.