It's possible that the creator of such a fanfic is trying to make a statement about the power dynamics in the Naruto world. Maybe they think that Naruto and Sasuke's power could lead them to do something unthinkable like killing Sakura. Or it could simply be a creative exercise in exploring a completely different narrative, even if it goes against the established characters' personalities.
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.
If in a Sasuke fanfic, one possible reason could be unrequited love. If Sakura feels that Sasuke will never return her love and she has exhausted all hope, she might sink into despair. Another reason could be if she feels she has failed Sasuke in some way, like not being able to protect him or help him in his goals. Maybe she blames herself for his continued pain or suffering and sees no way out but to end her own life.
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.
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.
One possible reason could be that some fans might want to explore different character dynamics. In many fanfics, Sakura is often paired with Sasuke. But if the story focuses on Sakura avoiding Sasuke, it could be to break the typical mold. Maybe the writer wants to show Sakura's independence and growth outside of her relationship with Sasuke. For example, she could be on a journey of self - discovery and Sasuke represents a past she wants to move away from.
It could be because of a dark power corrupting Sasuke. Maybe an ancient evil force takes over him and makes him see Sakura as an enemy. In some fanfics, this kind of external influence can completely change a character's actions. Also, it might be related to Sasuke's pursuit of power. If he believes Sakura is standing in the way of his ultimate power - seeking goal, he could be driven to kill her.
One possible reason could be Sasuke's focus on his revenge. His thirst for vengeance against Itachi might make him blind to Sakura's feelings and neglect her as he is constantly preoccupied with getting stronger to achieve his goal of revenge.
Maybe to explore different character arcs. The writer might want to see how Sakura would develop as a character if she strayed from her loyalty to Sasuke. It could also be a way to introduce new characters or relationships into the Naruto fanfic world.
Maybe Sasuke goes too far in his pursuit of power and tries to harm someone Naruto cares about deeply in the Forest of Death. Naruto, in a fit of rage and to protect the person, kills Sasuke.
One reason could be if Sasuke was somehow possessed by a powerful and evil force during the Chunin Exams. Naruto might see no other way to stop this threat and be forced to kill Sasuke to protect the village and others. Another possibility is a huge misunderstanding. For example, if Sasuke was framed for a crime he didn't commit and Naruto was misled into believing he was a danger.