It could be due to over - exertion during a difficult mission. Naruto often pushes himself to the limit, and this time it might have taken a toll on his body, resulting in a high fever.
Maybe he was poisoned during a battle. The poison could be slowly affecting his body and causing a fever as his body tries to fight it off. In fanfiction, the poison could be something unique created by an enemy ninja with special properties.
It could be the Hidden Leaf Village's council. If they were to unjustly accuse Naruto of a serious crime he didn't commit, like being a traitor, and try to imprison or execute him, that would surely make him lose it. He has always strived to protect the village, and such a betrayal from its leaders would be a huge blow.
Iruka - sensei could be an interesting option. He was Naruto's first teacher and has always had a soft spot for him. He would bring the warmth and comfort of a father figure. He might not have the advanced medical skills like Sakura, but he would stay by Naruto's side, tell him stories to keep his spirits up, and do whatever he can to help Naruto get better.
Danzo is another suspect. He has his own dark ways and has made decisions that could easily piss Naruto off, like using underhanded methods against his friends or the village.
One idea could be that Naruto gets a high fever right before a crucial mission. His friends, like Sakura and Kakashi, have to figure out how to complete the mission without him or find a way to get him better in time. Another plot could involve Naruto's high fever causing him to have strange dreams that give him insights into some hidden jutsu or mystery in the ninja world. Maybe his fever is the result of a new enemy's attack, like a poison that also affects his chakra flow, and the story could revolve around finding the antidote and defeating this new threat.
One common theme is friendship. When Naruto has a high fever, his friends always come to his aid, showing the strong bonds in the Naruto world. For example, they might bring him medicine or stay by his side to protect him.
Perhaps in the fanfiction world, Bella caught a mysterious disease that's specific to that fictional universe. It could also be that she overexerted herself, like using her special powers too much if she has any in the story. Stress can also be a factor. If she's been through a lot of emotional turmoil, like a fight with a loved one or facing a big threat, her body might react with a fever.
Sasuke could be a possible cause. If Sasuke were to go back on his word about protecting the village or if he were to harm their friends again, Naruto would be pissed. Their relationship is complex, and Sasuke's actions often have a strong impact on Naruto.
It could be Orochimaru. He has always been a source of trouble and if he manages to pull off some really devious plan that directly affects Naruto or his loved ones, it might cause Naruto to snap.
Madara Uchiha could also be a likely cause. If he somehow managed to return or had a long - planned scheme that involved breaking Naruto's sanity. He was a very powerful and devious foe who could use his knowledge of the ninja world and its powers to target Naruto's mental stability.