There are several motives that could be explored in such a fanfic. Sasuke might be influenced by a new ideology that deems Naruto as a danger to the village or the ninja way. He could also be under the influence of a powerful and evil entity that forces him to kill Naruto. Another motive could be that Sasuke's envy of Naruto's popularity and power gets the better of him, and in a moment of weakness, he decides to end Naruto's life. Also, in some fanfics, it could be a sacrifice Naruto makes where Sasuke is the one who has to do the deed, though this is a more complex and less common motive.
One possible motive could be power. In some fanfics, Sasuke might be driven by an insatiable thirst for power and see Naruto as an obstacle. Another could be revenge, perhaps believing Naruto has wronged him in some way in that alternate story. Or it could be a matter of being corrupted by dark forces, which make him turn against Naruto.
One possible motive could be a dark magic or mind - control situation. Maybe an enemy has the power to control Naruto's actions and forces him to kill Sasuke against his will. Another could be a miscommunication where Naruto believes Sasuke has done something unforgivable, like harming the village in a way that Naruto can't overlook.
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.
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.
One possible motive could be a dark or alternate universe take. Maybe in this fanfic's world, there is some sort of dark magic or mind control that forces Naruto to do it against his will.
It could start with a rift between them that becomes unbridgeable. Sasuke might side with a group that Naruto is sworn to oppose. Their ideological differences grow to such an extent that they end up in a final battle. Naruto, with a heavy heart, kills Sasuke perhaps because Sasuke refuses to back down and his actions are endangering too many lives. This would be a tragic departure from the original story where their relationship was centered around mutual understanding and redemption.
One possible motive could be that Sakura is brainwashed. Maybe an enemy uses some kind of mind - control jutsu on her and she becomes a puppet to kill Sasuke. Another could be extreme jealousy. If she felt that Sasuke was slipping away from her in some way, in a very dark and twisted version of the story, it could lead to her killing him.
Perhaps in a fanfiction where the world has been completely turned upside down. If Sasuke had been tricked into becoming an unstoppable villain who was about to destroy the entire ninja world, and Sakura was somehow aiding him (maybe under a genjutsu), Naruto might feel he had no choice but to stop them by killing. Another reason could be a broken heart. If Naruto loved Sakura deeply but she constantly rejected him and chose Sasuke, and then Sasuke and Sakura betrayed him in some way, his anger and pain could lead to such a drastic act.
One possible motive could be that Sasuke is so consumed by his thirst for power and revenge that he sees Sakura as a liability or a distraction. He might think that she would try to stop him from leaving the Leaf Village to pursue his own dark path, and in his warped state of mind, decides to eliminate her.
It could also be related to a prophecy or a pre - determined fate in the fanfic's plot. There might be some kind of dark prophecy that says Kawaki has to kill Naruto to prevent a greater evil. Or perhaps Kawaki is being controlled by an external force that has a vendetta against Naruto and uses Kawaki as a tool to carry out the murder.
Another motive might be related to some dark power corrupting Team 7. This power could have twisted their minds and made them see Kakashi as an obstacle in their path to achieving ultimate power. It could be something like the curse mark in the original Naruto series but even more powerful and insidious.