One possible reason could be that Naruto has a stronger willpower in the fanfic. His never - give - up attitude might be enhanced, allowing him to push past his limits more easily than Sasuke. For example, he might have an even deeper connection to the Nine - Tails' power, enabling him to draw on it more effectively in battles.
In some fanfics, Naruto's character development might be focused on his physical and mental growth in a way that surpasses Sasuke's. He could be depicted as having a more natural affinity for chakra control and a greater understanding of the nature of chakra, which makes him stronger when it comes to combat and other ninja skills.
Maybe in these fanfics, Naruto has received some unique training that Sasuke didn't. This special training could have unlocked new abilities or enhanced his existing ones. Like he could have trained with a hermit who taught him some ancient and powerful jutsu that gives him an edge over Sasuke.
It could also be that the writer wants to subvert the traditional power dynamics. In the original series, Sasuke is often seen as very powerful. But in this fanfiction, Sakura might be stronger because she has a stronger willpower. She could be more determined to protect her loved ones and this gives her an extra boost in strength. For example, her love for the village and her friends drives her to train harder and unlock new levels of power.
One possible reason could be that Naruto has access to some new and powerful jutsu. Maybe he discovers a secret family technique or is taught by a very powerful sage. This new knowledge gives him an edge over Kakashi.
One possible reason could be that Naruto has developed some new and extremely powerful jutsu in the fanfiction. Maybe he has found a way to combine his Sage Mode with his Kurama chakra in an even more efficient and powerful way that gives him an edge over Madara.
One reason is that Naruto has the Nine - Tails' chakra. In fanfic, this power can be further enhanced or manipulated in ways that make him far more powerful than Sasuke. Another reason could be his more outgoing personality. He might be able to form alliances more easily, leading to him having more resources and power - ups at his disposal.
One reason could be Naruto's unwavering determination. He has always been able to push past his limits. In many battles, his willpower has been a key factor in his victory. Another could be his unique chakra nature and the amount of chakra he has at his disposal. Naruto has a vast reserve of chakra, which gives him an edge in long - drawn battles. Also, his ability to form strong bonds with others might contribute. These bonds could potentially unlock new powers or give him the strength to fight against Kaguya.
It could also be due to a misunderstanding. Perhaps there is some misinformation spread about Sasuke in the fanfiction, like false rumors that he has a hidden and malevolent plan. Naruto, being someone who values their friendship deeply, would be scared at the thought of Sasuke turning into an enemy because of these untrue stories.
One reason could be Sasuke's thirst for power. If he believes Naruto is the only obstacle in his path to ultimate power, he might be driven to kill him. In some fanfictions, Sasuke may be influenced by a dark entity that twists his mind into thinking Naruto is a threat that needs to be eliminated.
Another reason might be related to their different ideologies within the ANBU. Naruto may have believed in a more collaborative and friendly approach within the organization, while Sasuke might have been more focused on individual achievement and power. This fundamental difference could lead to Naruto hating Sasuke in the fanfiction.
One possible reason could be to protect Hinata. Maybe Sasuke has unknowingly made a move or decision that Naruto perceives as a threat to Hinata, so he scares Sasuke to make him back off.
Maybe Naruto was trying to protect Sasuke from a certain danger. There could be a curse or a powerful enemy that targets male shinobi. So, Naruto uses a risky jutsu to transform Sasuke into a girl to keep him safe. Or it could be that Naruto found a strange ancient scroll with a transformation technique that he thought was something else and when he used it on Sasuke, it turned him into a girl.