In this fanfiction, it might be a new character. This new character could be jealous of Sonic's popularity and decides to take over his identity. They might have studied Sonic closely and learned his mannerisms to be a convincing imposter. Another possibility is that it could be a character from an alternate dimension who accidentally or purposely switches places with Sonic and then tries to keep up the act in Sonic's world.
There are several candidates. A power - hungry villain who wants to rule Sonic's world by taking his identity is a likely option. It could also be a shape - shifter who just wants to have some fun at Sonic's expense. Or perhaps a character who was wronged by Sonic in some way and is seeking revenge by replacing him and ruining his reputation among his friends and the inhabitants of his world.
It could be one of Sonic's old enemies who found a way to transform into him. Maybe Dr. Eggman created a sophisticated robot that looks and acts like Sonic.
In such a fanfiction, Sonic might face challenges like his friends being deceived by the imposter. His reputation could be at stake as the imposter might do bad things in his name.
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.
Dr. Eggman could be the antagonist. He's always trying to defeat Sonic, and shooting him could be part of one of his evil plans. Maybe he developed a new weapon specifically designed to take Sonic down.
Obviously, Sonic and Metal Sonic are the main characters. Sonic is the one being framed, and Metal Sonic is the one doing the framing.
It could be Dr. Eggman. He's always been after Sonic and trying to defeat him. Experimenting on Sonic could be his new way to find Sonic's weaknesses or to gain his powers for himself.
An old, retired hero. This hero, having seen Sonic's deeds, decides to take him under his wing. He could teach Sonic about the true meaning of heroism, based on his own experiences. It would be a story of passing on the torch, with Sonic learning valuable lessons from someone who has been through many battles and emerged victorious.
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.
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.
In this fanfiction, the Chaotix detective agency could also play a role in taking care of Sonic. Vector might not be the best at medical stuff, but he could use his detective skills to find out the source of Sonic's illness. Espio could use his stealth to keep an eye on Sonic's surroundings, and Charmy could keep Sonic's spirits up with his energetic personality.