A rogue robotic entity could be the main antagonist. This entity has the ability to roboticize other beings and views Tails as a prime target. It wants to use Tails' body as a vessel to spread its robotic influence further, so it sets out to roboticize him and then use him as a tool for its own dark purposes.
One possible plot could be that Tails is captured by an evil scientist. The scientist then roboticizes him against his will. Tails has to struggle to keep his original self and memories while being forced to do the scientist's bidding. Eventually, he might break free from the robotic control through the power of friendship with Sonic and the others.
Dr. Eggman could still be the main antagonist. Even if Tails turns evil, Eggman might see him as a threat to his own evil plans. He could try to stop Tails while also taking advantage of the chaos Tails is causing among Sonic and his friends.
Dr. Eggman could be a likely main antagonist. He might use his cunning and various inventions to manipulate the situation and make it seem like Tails or Rouge are traitors in order to further his own evil plans, like taking over the world or stealing some valuable chaos emeralds.
One possible plot could be that Sally is roboticized against her will. She then has to struggle to retain her humanity while dealing with the new abilities and limitations of her robotic form. Maybe she tries to find a way to reverse the process.
Sonic would be a likely main caregiver. He and Tails are very close friends. Sonic would use his speed to quickly get any medicine or supplies that Tails needs.
Fans of Sonic who have a creative streak and an interest in exploring different scenarios for the character might write it. They could be young writers who are really into the Sonic universe and want to put their own spin on things.
In addition to Sally, there could be other robotic characters in the fanfiction. Maybe there is a group of robots that Sally meets after being roboticized. They could either be friendly and help her understand her new state, or be hostile and see her as an outsider. And of course, her family members could also be characters, dealing with the changes in Sally.
Madara Uchiha could also be the main antagonist. Even if he was defeated before, in this fanfiction, he could come back with a new plan related to the Ten - Tails. He might want to use Naruto as a vessel to fully revive himself and then take over the Ten - Tails' power.
Another option is a group of anti - magic fanatics. They view Percy's wings as an abomination because they are a result of magic. They hunt Percy down, believing that by getting rid of him and his wings, they are protecting the world from the 'evils' of magic.
It could still be Hawk Moth. Since Nathalie has been working with him, getting a Miraculous might make her a threat to his plans, so he could turn against her and become the main antagonist.