Maybe there's a new character, a mad scientist who has been observing both the Sonic and Bendy universes. He creates a device that can merge the two worlds in a chaotic way, causing disasters in both. He believes that by doing this, he can become the ruler of the combined universe. Bendy and Sonic must stop him before the two worlds are completely destroyed.
Dr. Eggman could team up with a Pokemon villain like Team Rocket. They could combine their technology and evil plans. Eggman might use Team Rocket's knowledge of Pokemon to capture strong Pokemon and use them in his machines, while Team Rocket could benefit from Eggman's advanced robotics to create more powerful devices for stealing Pokemon.
Dr. Eggman would be a likely main villain. He might be the one who devises a plan to make Sonic fat, thinking that it will slow him down and make it easier for him to be defeated.
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.
It could be Orochimaru from Naruto teaming up with Dr. Eggman. Orochimaru is always seeking power and new forms, and Dr. Eggman wants to take over the world. Together, they could create some really dangerous machines and jutsu combinations to try and achieve their goals.
Perhaps a dark sorcerer who has cursed the planet. The sorcerer sees Sonic and his friends as a threat to his rule over the planet and tries to stop them from leaving or finding a solution to the planet's problems.
It could be Eggman. He might team up with some of the Justice League's villains, like Lex Luthor. Eggman could bring his mechanical creations and knowledge of chaos emeralds, while Luthor provides his strategic mind and resources. Together, they could pose a huge threat to both Sonic and the Justice League.
It could be a new villain created just for this fanfiction. Maybe a powerful wizard who wants to use the combined powers of Sonic Underground and Tails for his own dark magic. He sees their unique abilities as a way to gain ultimate power and they have to fight against his spells and minions.
Dr. Eggman could be a great main villain. He might have a new plan that involves both the power of Sonic Underground's music and the Chaos Emeralds that Shadow guards. He could try to create a device that amplifies negative emotions through music and uses the Chaos Emeralds' power to spread chaos everywhere.
It could be Dr. Eggman. He might have manipulated Shadow into kidnapping Sonic. Maybe he promised Shadow something in return, like power - ups for his abilities. Dr. Eggman wants to study Sonic's speed and abilities, so he uses Shadow as a tool to get Sonic in his clutches.