One possible reason could be Sasuke's actions that Naruto deems too extreme for the safety of the village. For example, if Sasuke were to ally with a powerful enemy who plans to destroy Konoha. Naruto, being the protector of the village, might feel he has no choice but to kill Sasuke to safeguard his home and the people he loves. Another aspect could be a misunderstanding. Maybe Sasuke is framed for a heinous crime, and Naruto, without realizing the truth at first, believes he has to end Sasuke's life for justice. It could also be related to some dark power that has corrupted Sasuke's mind, making him a threat that Naruto has to eliminate to save Sasuke from himself in a rather extreme way.
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.
One possible reason could be a difference in their goals. Sasuke has always been on a journey of revenge and self - discovery. If in the fanfic, Naruto's path starts to conflict with Sasuke's in a way that Sasuke can't tolerate, he might leave. For example, if Naruto decides to fully side with the village elders whom Sasuke distrusts, Sasuke could see this as a betrayal of their friendship and leave. Another reason could be an external threat that forces Sasuke to leave to protect Naruto. Maybe there's a powerful enemy that specifically targets Sasuke and he doesn't want Naruto to get caught in the crossfire, so he leaves without explanation to keep Naruto safe.
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 possible reason could be that Sasuke might have gone too far in his pursuit of power even after the war. He could have been a threat to the newfound peace in the ninja world, and Naruto, as the protector of peace, might have felt he had no other choice.
Well, it could start with Sasuke approaching Naruto in a rather secretive way. He would lay out his plan about joining Team Hebi, highlighting the advantages. Naruto would be skeptical at first. He loves his friends in Konoha and doesn't want to abandon them. But Sasuke might argue that by being in Team Hebi, they can protect Konoha in a different way. As for the Team Hebi members, Suigetsu might be excited as he sees Naruto as a strong addition. Karin would be more cautious as she's worried about Naruto disrupting the group. Jugo might be indifferent at first. The fanfic could then focus on Naruto's journey of making this difficult decision, weighing his loyalty to Konoha against the potential of achieving more with Sasuke in Team Hebi.
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.
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.
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.
One possible reason could be that it goes against the original dynamic between Naruto and Sasuke. In the original story, their relationship is based on a deep male - male bond of rivalry and friendship. Changing Sasuke to a female might disrupt that established connection.
The impact on Hinata would also be significant. She understands Naruto's sense of justice but would also be worried about the emotional toll it would take on him. She might try to comfort Naruto while also being conflicted about the whole situation. For the other ninja clans in Konoha, it could lead to internal disputes. Some clans might see Naruto's action as necessary for the safety of the village, while others might view it as a breach of the bond between comrades. And for the ninja world at large, it could change the power balance. Sasuke was a very powerful ninja, and his death at Naruto's hands could make other villages either fear Konoha more or see it as a place where even the closest friends can turn on each other.