Perhaps there's a plot device where an external force is controlling Erza's actions. This force could make her act against her will and harm Natsu. In the world of fanfiction, dark magic or mind - controlling entities are common tropes. So, it's possible that Natsu gets hurt as a result of this external influence on Erza.
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.
It could also show the complexity of their relationship. Maybe Erza's actions are out of her own insecurities or fears, and Natsu getting hurt is a consequence of her not being able to handle those emotions properly. This would mean that their relationship is not just about friendship or comradeship, but also about understanding each other's inner turmoil.
One possible plot could be that Natsu gets hurt during a battle with a powerful dark mage. His friends then have to find a way to heal him while also dealing with the threat of the mage still being around. Maybe they search for a rare magical herb or seek help from a reclusive healer.
It could be that Erza scolds Natsu too harshly for something he did wrong. Natsu, who might be more sensitive than he seems, could end up crying from the severity of her words.
One possible reason could be that Erza is focused on her own goals and career in the Fairy Tail guild. She might see a relationship as a distraction at that moment. For example, she is always striving to be stronger and take on more challenging missions. Another reason could be that she may not view Natsu in a romantic way but more as a close friend and guildmate. Maybe she has a different ideal type in mind, someone more calm and studious rather than Natsu's brash and impulsive nature.
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 could be that Erza might have taken on a dangerous mission alone without informing Natsu. Natsu is protective of his friends and would get angry if he thought Erza was putting herself in unnecessary danger.
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.
Well, in some fanfictions, it could be that Lucy is under a curse. This curse makes her act out of character and she ends up hurting Natsu. Maybe she is cursed to attack the closest person to her, and at that moment, it's Natsu. Or it could be a situation where Lucy is forced to choose between saving herself and Natsu in a dangerous situation, and her choice, even if it's to save herself, could be seen as hurting Natsu. Also, there could be a plot where Lucy is brainwashed by an enemy who wants to break the bond between her and Natsu, and as a result, she causes him harm.
Another possibility is that the fanfiction writer wants to explore a different side of their relationships. By having Hermione and Ron hurt Harry, it shows the complexity of human (or in this case, wizard) emotions. It could be a way to show that even the strongest friendships can have cracks and that mistakes can be made. It also allows for character development as Harry has to deal with this new situation, and Hermione and Ron may later realize their mistakes and try to make amends.
In many fanfictions, Natsu and Erza often have a complex relationship. Natsu is usually depicted as a bold and passionate character, while Erza is strong - willed. Their relationship might start from comradeship within the guild. Some fanfictions may explore how they gradually develop deeper feelings for each other, like through shared adventures and facing challenges together. This can lead to a mutual understanding and respect that could potentially turn into a romantic relationship.