It could be another animal in the neighborhood. Maybe there's a territorial cat that doesn't like Jojo and Saphie being around. This cat could attack Jojo when they cross into its territory.
Another scenario could be that there is an antagonist in the story, someone who doesn't like Saphie because of her unique appearance. Jojo, being Saphie's friend, stands up to this antagonist. This results in Jojo getting hurt in the confrontation. The story could then focus on how Saphie tries to help Jojo recover and seek revenge on the one who hurt him.
Maybe Joho's sickness could be a magical ailment that only Saphie, the one - eyed cat, can cure. For example, Saphie might have some special powers that are connected to her one eye, like the ability to see into the spirit world where the source of Joho's illness lies.
The main characters are clearly Joho and Saphie. Joho is the one who gets sick, so he's likely to be at the center of the story's problem. And Saphie, the one - eyed cat, seems to be an important figure who will probably play a big role in dealing with Joho's sickness.
It could be a new, self - created villain. This villain might have been training in secret for years, specifically to defeat Goku. He could have studied all of Goku's moves and weaknesses and then launch a surprise attack that causes Goku to get hurt.
It could be an antagonist. Some villain who has a grudge against Toby or the group he is associated with. This villain might see Toby as an obstacle and deliberately target him to cause harm.
Physical hurt might come from a powerful magic spell. Let's say an evil sorcerer casts a spell that drains Yami's energy and causes him pain. His struggle to overcome this and regain his strength could be a central part of the fanfiction.
Well, in a fanfiction plot, Nicole could be hurt while trying to protect her partner. For example, if there's a bomb threat in a building where they are. Nicole would shield her partner from the blast, resulting in her getting seriously hurt with burns and fractures. Or perhaps she gets into a car accident while rushing to a crime scene because of a mechanical failure in her vehicle.
One possible plotline could be that Tohru gets physically hurt during an accident while helping out at the Sohma house. Maybe she's climbing a ladder to fix something on the roof and slips, resulting in a sprained ankle or a cut. Another could be that she gets emotionally hurt when she overhears some of the Sohma family members saying unkind things about her, not realizing she can hear them. It could make her question her place in their lives.
Yuki would likely be very concerned. He has a soft spot for Tohru and would probably rush to her side, trying to find a way to help. He might even blame himself if he thinks he could have prevented it. Kyo, on the other hand, would initially be angry, but that's just his way of showing worry. He would be more hands - on in getting her the help she needs.