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 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.
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.
Maybe an evil artist from another dimension. This artist is jealous of Nathanael's pure creativity and the unique power of his miraculous. They come to Nathanael's world to steal his ideas and use his miraculous for their own dark purposes, like creating chaos and destruction through art.
Maybe the main antagonist is an old enemy of Robin's who becomes jealous of his new powers. This enemy then devises a plan to steal Robin's powers or at least neutralize them so that he can regain his former status as the top threat. He could be a powerful martial artist or a criminal mastermind with a large network of henchmen.
It could be a jealous rival. This rival might be envious of mankae's popularity or achievements. So, they set him up to get arrested by providing false information to the police. They want to see mankae's downfall and think that getting him arrested is the best way to achieve this.
It could be Orochimaru. Since he has always been interested in powerful ninja abilities, he might see Sakura with the Sharingan as a new target. He could try to steal the Sharingan from her to add to his own collection of powerful jutsus and abilities.
A power - hungry politician in Nero's world could be the main antagonist. They see Nero as a threat to their power or as an easy target to gain more influence. They manipulate situations to make it seem like Nero has done something wrong.