Well, often in Sonic gets hurt fanfiction, a common theme is the reaction of the Sonic universe characters. Characters like Knuckles might be in disbelief at first that Sonic could be so hurt. There's also the theme of Sonic's internal struggle. He might be frustrated that he can't be as active as he wants. And sometimes, there are themes related to the cause of the injury, like if it was a powerful new enemy that managed to harm him, which then sets up a revenge or recovery arc.
Well, Sonic is a hero at heart. So when Amy gets hurt, he would first assess the situation calmly, but inside he'd be worried. He'd make sure she was stable and then look for the cause of her injury. If it was an enemy, he'd go after them. But he'd also be very gentle with Amy, talking to her softly and reassuring her that she'll be okay. He'd do whatever it takes to see her back on her feet again, like finding special herbs or items that could speed up her healing process.
Writers create tension by showing Sonic's pain and struggle. For instance, if he's trying to run but the injury stops him, it builds tension. Also, when his friends are worried about him, like Tails panicking as he tries to figure out what's wrong with Sonic, that adds to the tension.
One possible storyline could be that Amy gets hurt while trying to protect Sonic from an enemy. Maybe she jumps in front of a powerful attack meant for Sonic. Another could be that she gets injured during a dangerous adventure in a new, uncharted zone. For example, she might fall into a hidden trap.
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.
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.
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.
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.