Maybe Sonic's friends will take care of him. They could bring him medicine and make sure he rests. For example, Tails might use his inventions to find a quick cure.
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.
Sonic himself, of course. And his best friend Tails is very likely to be there. Tails is always by Sonic's side and would surely be there when Sonic is sick.
One possible plot could be that Sonic catches a strange virus that slows down his super speed. His friends like Tails and Knuckles would then have to find a cure while protecting Sonic from his enemies who might see this as an opportunity to attack.
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.
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.
In addition to his family and friends, the medical ninja in the village would be involved. They would be the ones to accurately diagnose Boruto's condition. Shizune, for example, could come and check on him, using her vast medical knowledge. And the other young medical ninjas might learn from this case, as Boruto's illness could be something new or unusual, so they would be eager to assist and gain experience while taking care of him.
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.