Perhaps it's a result of a failed experiment by one of the village's scientists or ninjas. They could have been working on some kind of time - space ninjutsu and something went wrong. Naruto just happened to be in the wrong place at the wrong time. It might be someone like Shikamaru, who is known for his intelligence and might have been trying to create a new strategy involving time manipulation but it backfired on Naruto.
There could be a mysterious and ancient force at work. It could be a curse placed on Naruto because of his status as a Jinchuriki. Some ancient entity that doesn't like the idea of a human - tailed beast combination might have used the time loop as a way to keep Naruto trapped, hoping to break his spirit and ultimately separate him from the Nine - Tails.
Danzo could also be the one to make Naruto angry. Danzo's underhanded tactics and secrets might be exposed in the fanfiction, and if they were to directly harm Naruto's friends or the village, Naruto would be furious at his actions.
Maybe in the time loop, Naruto discovers new aspects of his chakra. He could find out that he has a hidden power that he was unaware of before. This could lead to him training in new ways during the loops to master this power. It might also change his relationships with his friends and teachers as they notice his new abilities and the mystery behind them.
Hermione Granger would definitely be a huge help. She's extremely intelligent and well - read in magic. She could study all the books in the library to find a way to break the time loop. Ron Weasley could also be important. His loyalty and courage would keep him by Harry's side through all the loops, and he might come up with some practical, if not always academic, solutions.
Sasuke could be the cause. If Sasuke were to betray Naruto again in the fanfiction, it would surely make Naruto pissed off. Their relationship is complex and Sasuke's actions have a big impact on Naruto.
A mysterious new enemy that has infiltrated the village could be the cause. This enemy might be on a mission to disrupt the balance in the ninja world and sees Sarada as an obstacle. They could attack her when she is alone or on a solo mission. Their motives could be related to some ancient grudge against her family or the village as a whole.
Hawkmoth, of course. He's always looking for opportunities to akumatize people, and Ladybug would be a huge prize for him. If he could find the right moment when Ladybug is feeling vulnerable, like after a big defeat or a personal crisis, he could send an akuma her way.
Sasuke could also be a character who breaks the time loop. He is highly intelligent and has a thirst for power and knowledge. If he realizes that he is in a time loop, he would likely be very intrigued and start investigating. His Sharingan might give him some insights into the nature of the loop and help him find a way to break it.
It could also be a new, unknown enemy. Maybe there's a secret organization that emerges in the fanfiction that has a vendetta against those with electric powers like Michael. They could target him specifically and cause him harm.
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.
Naruto himself is often the central character. Since it's his time loop, his actions and growth throughout the repeated scenarios are what drive the story. Fans enjoy seeing how he uses his knowledge from previous loops to change things.