Another possibility is that a new dark force, not related to Voldemort, emerges. This new entity could target Harry because they see him as a threat to their plans. They might have unique and powerful magic that they use to seriously wound Harry, leaving him in a state where his friends and the wizarding world have to figure out how to counter this new threat.
It could be a rogue Death Eater who has been hiding and waiting for the right moment to strike at Harry. They might use some forbidden dark magic to seriously harm him.
In some fanfictions, Harry could be seriously hurt during a dark magic attack by a new and powerful dark wizard. For example, he might be hit by a powerful curse that drains his magic and leaves him in a critical condition.
There's also the possibility that it's not a dark force at all. It could be a well - meaning but misguided wizard who accidentally causes Harry to be badly hurt. For instance, during a training session that goes wrong or while trying to perform a difficult spell to protect Harry but ends up harming him instead.
It could be a rogue Death Eater who managed to catch Harry off - guard. Maybe they were lying in wait and launched a surprise attack when Harry was alone, away from the safety of Hogwarts.
It could be an old enemy like Luke. He has always had a vendetta against Percy and would not hesitate to cause him harm. Maybe Luke has some new evil plan and hurting Percy is part of it.
Another possibility is a jealous student at Hogwarts. There are always students who might be envious of Hermione's academic achievements. They could set up a prank or a trap that goes wrong and ends up hurting her. For example, a student who is tired of Hermione always getting the top grades in Potions might tamper with her cauldron during a class experiment, resulting in an explosion that hurts her.
There's also 'When Pain Meets Comfort'. Here, Harry is suffering from the after - effects of a dark spell. James Potter, who has been observing Harry from a sort of spiritual plane, finally manages to break through and reach Harry. He takes Harry to a magical place where they can talk and James heals Harry's wounds, both visible and invisible, with his paternal love.
One plot could be that Harry is seriously injured during a battle with a new dark wizard who has emerged. His friends then have to find a rare magical herb to heal him while fending off attacks from the wizard's followers. Another could be that he gets injured in a mysterious accident during a dangerous potion - making experiment at Hogwarts, and it's up to Hermione to figure out the antidote before it's too late.
In the fanfiction, it might be that a mysterious figure is responsible. This person could have a vendetta against Amy's family or the stables she works at. They could set up a trap, like loosening a fence rail that Amy's horse jumps over, causing the horse to stumble and Amy to be thrown and badly injured.
It could be a rival from another house. For example, a jealous Slytherin who wants to take Ginny out of the Quidditch game. They might use some underhanded tactics to make her broom malfunction and cause her to get hurt.
Maybe it's a jealous acquaintance. If Kagami is really good at something, like she's a star in a particular activity, someone who is jealous of her success might set up a situation where she gets hurt. For instance, they could tamper with her equipment in a way that causes her to have an accident.