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.
There could be a mechanical entity created from the planet's misfortunate energy. It views Sonic and his friends as intruders and tries to destroy them to protect the planet's 'negative equilibrium'.
In this 'sonic x planet of misfortune fanfiction', Sonic could be separated from his friends upon arriving at the planet. He then has to endure a series of misfortunes all by himself. But as he overcomes each obstacle, he becomes stronger. Eventually, he reunites with his friends and they all find a way to leave the planet.
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.
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.
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.
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.
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.
Mr. Sinister would be a great main villain. He's always had his own sinister plans for mutants. In a 'Termination' scenario, he could be taking advantage of the chaos to further his experiments on mutants, seeing it as an opportunity to create more powerful mutants under his control.
A new villain could be created specifically for this fanfiction. This villain could be a being that feeds on the chaos between the two different universes. It has the ability to disrupt chakra flow in Naruto's world and nullify magic in Lulu's world. Naruto and Lulu would have to figure out how to work together to stop this entity before it destroys both of their homes.