It could be an enemy dragon. There are many rival dragons in the Fairy Tail universe, and if they see Natsu with Igneel, they might target Natsu to get to Igneel. Dragons can be very territorial and protective of their own, and an enemy dragon may see Natsu as a weak point to attack Igneel through.
One possibility is that Igneel would immediately go into a protective mode. He might use his dragon powers to heal Natsu if he has such abilities. Since they have a strong bond, Igneel would be enraged at whatever caused Natsu to get hurt and would seek revenge. He could also stay by Natsu's side until he recovers, providing warmth and comfort as dragons are often associated with being a source of strength and protection.
One possible reason could be a misunderstanding during a mission. Maybe Erza's actions were misinterpreted by Natsu, leading to him getting hurt, either physically or emotionally.
He could marry an original character created specifically for the fanfiction. This character could be a powerful mage from a far - off place who crosses paths with Natsu during one of his adventures.
One of the senior and more experienced members of the guild. They have seen a lot and know how things should be done in the guild. If Natsu acts in a way that goes against their long - established ways, they would not hesitate to berate him.
Lucy could be a main character. Since she's often by Natsu's side, she would likely be deeply involved in his recovery. She could use her celestial spirit magic to try and protect him while he's injured or search for a way to heal him.
One possible reason for Natsu to return badly hurt in a fanfiction could be a very tough battle. Maybe he faced an extremely powerful enemy that was far beyond his initial expectations. For example, if he encountered a new type of dark mage with some unknown and dangerous magic. This could lead to him getting seriously injured and having to struggle to return.
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.