It could be a new character, perhaps a jealous rival who is envious of Sonic's speed and popularity. This character might create a situation where Sonic gets fat, like spreading some kind of 'fat - inducing' virus in Sonic's food supply.
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.
Maybe in the 'sonic gets fat fanfiction', Sonic discovers a new type of power - up that gives him super strength but as a side effect, it makes him gain a lot of fat. He then has to learn to control this new power without sacrificing his speed and agility. He might go on a journey to find a way to reverse the fat gain while using the power for good.
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.
It could also be a new villain. Maybe someone who has been waiting for Sonic to be in a vulnerable state. This new villain could have a special power or weapon that is more effective against Sonic as a kid. For example, a device that can slow down Sonic even more or nullify his powers temporarily. They might target Sonic not just because of his weakened state, but also because they know that his friends will be distracted trying to help him get back to normal.
It could be an evil scientist. This scientist was conducting experiments to create superhumans, but his experiments went wrong. Now, he's jealous of Marco's natural - born powers. So, he tries to capture Marco and study him to find a way to replicate his powers for himself. The scientist creates all kinds of dangerous traps and robotic minions to try and catch Marco.
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 some of the lesser - known badniks that team up to bully Sonic. Since they can't defeat him on their own, they figure that by ganging up on him and bullying him, they can at least make his life difficult.
One possibility is Dr. Eggman. He has always been after Sonic and wants to stop him. Kidnapping Sonic would be a way for him to achieve his evil goals.