Perhaps the true antagonist is a dark force that has been awakened by the imbalance in the Black Knight's world. This force slowly takes over the minds of the characters Sonic meets, and he has to find a way to stop it before it consumes everything, including himself.
The main antagonist could be an evil sorcerer who has corrupted the Black Knight and is using him to carry out his dark plans. This sorcerer could be after Sonic's speed power to enhance his own magic.
Maybe the Akatsuki as a whole. They are a group of powerful and dangerous ninjas. The Black Knight's presence might disrupt their plans to collect all the tailed beasts. They would see him as an obstacle and try to eliminate him. For example, Pain might think the Black Knight is a threat to his vision of peace through pain and send his subordinates to fight him.
One idea could be Sonic having to face a new and more powerful dark version of the Black Knight. This would test his skills and force him to find new ways to use his speed.
Maybe the main antagonist is a scientist who has been experimenting with vampire-like powers and accidentally creates a powerful vampire - like monster. This monster then starts attacking the world, and Shadow, as a new vampire - hedgehog, has to stop it. The scientist might also be trying to cover up his mistake and will stop at nothing to keep Shadow from interfering.
There could be an interdimensional being that thrives on chaos. It sees the meeting of Jack Frost and Sonic as an opportunity to cause mayhem in both of their worlds. It starts by creating disasters in both the wintry realm of Jack Frost and the colorful world of Sonic. To stop it, Sonic and Jack Frost must figure out the being's weakness while also trying to protect their respective homes and friends.
A corrupted King Arthur could be the new villain. Imagine if the power of the Excalibur sword has turned him evil, and he now wants to rule the world with an iron fist. Sonic would have to find a way to break the curse on Arthur and stop his tyrannical rule.
The main characters are Sonic, of course. He's the fast - running hero who gets drawn into the world of the Black Knight. And Merlina, who has her own motives and powers within this world.
Dr. Eggman could be a great main antagonist. He could be using the chaos of war to further his own plans for world domination. He might be creating powerful war machines and using them to take over different regions, forcing Sonic and his friends to fight back to protect the peace.
A new character could be introduced as the main antagonist. For example, a being from another dimension who has been observing both Sonic's and Megaman's worlds. This being realizes that by combining the chaos energy from Sonic's world and the advanced robotics technology from Megaman's world, it can create a new, all - powerful empire. So it starts to manipulate events in both worlds to bring about this combination, while Sonic and Megaman have to stop it.
Dr. Eggman and Dr. Wily could team up. Dr. Eggman has his mechanical creations and knowledge of Sonic's world, while Dr. Wily is an expert in creating powerful robots in Mega Man's world. Together, they could be a formidable force against Sonic and Mega Man.
Well, obviously Dark Gaia itself could be the main antagonist. It has the power to cause chaos and destruction, and Sonic would have to stop it from wreaking havoc on the world.