Maybe Sasuke is possessed by an extremely powerful and evil entity that can't be exorcised. Naruto, after trying all other means to save his friend, might be forced to kill Sasuke to prevent the entity from causing more harm. This would be a very dark and tragic scenario where Naruto has to sacrifice his friendship for the greater good.
One possible motive could be if Sasuke was on a path of destruction that endangered the entire ninja world. Naruto, as the protector of peace, might see killing Sasuke as the only way to stop him. For instance, if Sasuke was about to unleash a powerful and uncontrollable jutsu that would wipe out many innocent lives.
Perhaps Sasuke is possessed by some extremely evil entity. And Kakashi, in an attempt to stop the entity from causing more destruction, decides to kill Sasuke. It could also be that Sasuke discovers some dark secret about Kakashi that Kakashi doesn't want revealed, and in a moment of panic and self - preservation, he kills Sasuke.
Well, it could be that Kakashi is under some sort of dark spell or curse that makes him see Naruto as a threat to the village. In some fanfictions, there might be a situation where the village's safety is at stake and Kakashi believes that sacrificing Naruto is the only way to save everyone. Also, it could be a case of false information. If someone convinces Kakashi that Naruto has turned evil and is about to cause great harm, he might take the drastic step.
In fanfiction, Naruto might kill Konoha if he's under some sort of mind control. Maybe an enemy manages to manipulate his thoughts and turn him against the village. Also, if Naruto experiences a great loss because of Konoha's actions or inactions. Say, if his friends are killed due to Konoha's negligence in protecting them, and he blames the village as a whole. Or if he realizes that Konoha's system is so corrupt that it's causing more harm than good to the world.
One possible motive could be Naruto's extreme sense of loyalty and friendship. He might believe that by sacrificing himself, he can save Sasuke from the darkness completely. He could think that his death would shock Sasuke into realizing the error of his ways and bring him back to the side of good.
It could also be a power play. In the Naruto universe, power is a big deal. Some might frame Naruto to get him out of the way in their pursuit of power. Since Sasuke has his own group of fans in the fic, they could be used as tools to achieve this by making it seem like Sasuke is against Naruto, when in fact it's all a setup.
One possible motive could be if Sasuke goes too far in his pursuit of power and becomes a threat to the entire ninja world that even Naruto can't reason with. Maybe Sasuke starts to kill innocent people without hesitation, and Naruto, as the protector of the village and the one who believes in peace, sees no other option but to stop him by killing. Another motive could be some kind of dark magic or mind control that makes Sasuke an uncontrollable force of destruction, forcing Naruto to take drastic measures.
One possible motive could be if his brother was somehow a threat to the village. Naruto is very loyal to Konoha, so if his brother was planning to destroy it or harm its people, Naruto might feel compelled to stop him at all costs.
It might be for Naruto's own good. Sasuke may believe that Naruto is on a dangerous path that will lead to his downfall. So he captures him to keep him from making bad decisions, like sacrificing himself for the village or something similar. He wants to save Naruto from himself in a sense.
One possible motive could be jealousy. If Kiba were to gain more recognition in the village than Naruto in the fanfiction world, Naruto's insecurities could drive him to do something drastic like killing Kiba. But this is a huge departure from his usual self.
Perhaps Fem Sasuke in this fanfiction has a different view of the world. She might believe that Naruto is a threat to her goals or to the future of the ninja world she envisions. It could also be that she has some deep - seated emotional pain that she blames Naruto for, and that leads her to kill him.