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 possible plot could be that Sonic is bullied by a new group of antagonists in his world. They might make fun of his speed, saying it's not all that great and constantly tripping him up during races. Another plot could be that Sonic is bullied by some of the other characters who are jealous of his popularity. They start spreading false rumors about him, which makes some of the animals in the forest start to avoid him.
I'm not sure specifically as there could be various interpretations in such a fanfiction. Maybe Metal Sonic sets Sonic up in a way that makes Sonic look bad to the other characters, perhaps by faking some evidence or causing chaos and making it seem like Sonic's fault.
He might also find some allies. Leo can look for friends or even adults who can support him. If he has a good friend, they can walk together and the bully might be less likely to target him. And if he tells an adult like a teacher or a parent, they can take steps to stop the bullying.
Positive Sonic fanfiction could be about Sonic mentoring the younger characters like Tails and teaching them important life lessons. Or it could be about Sonic and his friends having to solve a mystery in their world, like a strange disappearance of an important item or character. Fanfictions that show the characters growing and evolving in positive ways, such as Amy becoming more confident in her own abilities, are also excellent alternatives to inappropriate fanfiction themes.
Sonic would probably be very shocked at first. He trusts Amy, so her betrayal would be unexpected. He might initially try to talk to her to understand why she did it.
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.
I'm not entirely sure specifically as there could be many interpretations. It might be a fanfiction where Sonic, the character, experiences some sort of 'breaking' event. Maybe he gets injured, or his spirit is broken in some story - created - by fans.
Well, in this 'sonic gets roboticized fanfiction', it might explore the idea of Sonic's identity when he becomes robotic. It could show how his friends react to this new form. For example, Tails might be shocked at first but then try to find a way to reverse the roboticization. And Sonic himself could be struggling with feeling less 'alive' in his robotic state, all while facing new enemies or challenges that are related to his new robotic nature.