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.
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.
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.
Perhaps a rogue vampire who has his own agenda. He might be jealous of the red knight's power or status and constantly tries to undermine them. This vampire could be very cunning and not afraid to use dirty tricks to get what he wants.
Another possibility is a corrupted version of one of Sonic's friends. Maybe through some dark influence, like an evil Chaos Emerald, a friend turns on Sonic and blinds him. This would add an extra layer of drama as Sonic has to deal not only with his blindness but also the betrayal of someone he trusted.
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.
Dr. Eggman would be an obvious choice. Since Sonic is now in a more vulnerable human form, Eggman could see this as the perfect opportunity to finally defeat Sonic and take over the world. He might come up with new devious plans, like creating robots specifically designed to target a human Sonic.
Dr. Eggman would be a likely choice as he often causes trouble for Sonic. In the context of Secret Wars, he could have found a way to connect Sonic's world to other dimensions and start the wars to finally defeat Sonic once and for all. He might be using new and powerful machines he has created from the combined technology of different dimensions.