One reason could be Naruto's sheer determination. He has always been the one with an unwavering will, and in this fanfic, that might be the key factor. His never - give - up attitude gives him the extra boost to defeat Sasuke.
Naruto might have received some new power - up. Maybe he found a new type of chakra or a powerful weapon that gives him an advantage over Sasuke. His training could also have reached a new level, making his physical and ninjutsu skills far superior to Sasuke's at that moment in the fanfic.
Well, from a practical standpoint, comparing the two is like comparing apples and oranges. Their universes have different rules regarding power and physics. In a fanfic, though, the writer can manipulate the story to suit their desired outcome. Maybe Naruto uses his intelligence and strategic thinking along with his chakra powers to defeat Superman. It could be that the fanfic has Superman in a situation where his powers are nullified and Naruto is able to use his ninja skills to gain the upper hand.
One reason could be to create a lot of angst. If Sasuke cheats, it would deeply hurt Naruto and cause a rift in their relationship, which could lead to a lot of emotional turmoil for both characters. This would make for a very dramatic story.
A moment of desperation. For example, if one of them is about to die in the alley due to an injury or a curse. The other, in a rush of emotion, kisses them as a way to convey all the unsaid things, all the love and friendship that has been there all along.
One possible reason could be his thirst for power. He might see Naruto as an obstacle in his pursuit of greater strength. Maybe he believes that by eliminating Naruto, he can prove himself to be the stronger one and gain more recognition in the ninja world.
Maybe Naruto gets tired of always chasing after Sasuke. He has his own life and dreams too. He might think that he has sacrificed enough of his time and energy on Sasuke, and it's time to focus on himself and the village. He could start to believe that Sasuke has made his own choices and he can't keep forcing Sasuke to come back.
Some fanfic authors might write it as a form of wish - fulfillment. They might prefer the Naruto - Sakura relationship more than the Sasuke - Sakura one. So, they create a scenario where Sakura turns to Naruto in a romantic way. Additionally, it could be a way to explore the characters' personalities further. For example, how Sasuke would handle being betrayed and how Naruto would deal with being involved in such a situation. It gives a chance to dig deeper into their emotional and moral aspects.
In such a fanfic, one possible reason could be Naruto's feeling of being left out. Maybe he sees Sakura's constant focus on Sasuke and feels neglected in their friendship triangle. Another reason might be jealousy. If Naruto has unrequited feelings for Sakura, seeing her love for Sasuke could turn to hatred over time.
Another possibility is that Naruto was trying to protect someone else from Sasuke. Suppose Sasuke was on a path that would endanger another important character in the story, like Sakura. Naruto, in his eagerness to safeguard Sakura, might have accidentally hurt Sasuke while trying to stop him from taking any harmful actions.
One interesting way could be through the use of genjutsu. Naruto could trap Superman in an illusion where he believes he has lost his powers or is facing an unbeatable foe. Since Superman's mind is not immune to such psychic attacks in a fan - created scenario, Naruto could then use his physical attacks like Rasengan to finish him off.
One reason could be to create shock value. By having two main characters kill another important character, it grabs the reader's attention. Another could be to explore a very dark and alternate version of the Naruto universe. Maybe the writer wants to show how far characters could be pushed in extreme situations.