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.
One idea could be that Bendy and Sonic find themselves in a strange, in - between world where the art styles of their respective universes start to blend. They have to team up to find a way back to their own worlds. Maybe there are some glitches in this new world that they need to fix together.
The Devil could be the main antagonist. Since he is Cuphead's main enemy in his own game, he might follow Cuphead into Bendy's world. He could see Bendy's world as a new place to spread his evil and also wants to get revenge on Cuphead. He could start causing chaos in Bendy's world, which would force Cuphead and Bendy to team up against him.
The main villain could be an ink - blotted version of Maleficent. She has all of Maleficent's cunning and dark magic but now also has the ability to manipulate ink like Bendy. She wants to cover both the world of Bendy and Mickey Mouse in eternal darkness. She starts by corrupting some of the minor characters in both worlds and turning them into her minions. Bendy and Mickey have to work together to stop her before she can fully achieve her evil plan.
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.
Perhaps the Green Goblin could be the villain. He's a classic Spiderman foe and could pose a real threat to both Spiderman and the Shadow.
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.
In my opinion, Goku has more experience in fighting powerful opponents on a universal scale. He has fought against gods and demons. Sonic, on the other hand, mainly deals with threats to his own world. But Sonic's speed is not to be underestimated. He could potentially outmaneuver Goku and find a weakness. However, Goku can constantly increase his power during a fight. So, again, it's not clear who would win.
It could be Dr. Robotnik teaming up with the Fratellis. Dr. Robotnik might see the potential in the Goonies' treasure or the area they live in for his own evil plans. He teams up with the Fratellis who are already villains in the Goonies' world. Together, they create chaos and try to stop Sonic and the Goonies from achieving their goals, whether it's protecting the treasure or saving Sonic's friends.