It could be a way for the writer to explore a tragic or 'what - if' scenario. For example, if there was misinformation or a huge misunderstanding between Naruto and Neji. But still, it's a very unorthodox and shocking concept considering the original relationship between the two characters in the Naruto series.
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.
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 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.
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.
One possible motive could be revenge. If Pauna had done something really bad to Clarke or someone Clarke cares about in the fanfic's backstory, Clarke might feel compelled to kill Pauna. Another could be self - defense. Maybe Pauna was attacking Clarke and she had no other choice.
A possible motive could be that Naruto discovers some dark secret about Minato that makes him feel betrayed. For example, if he finds out that Minato was involved in some unethical experiments that led to the suffering of many people. Or perhaps Naruto is tricked by a powerful villain who manipulates his emotions and convinces him that Minato is the root of all his problems.
One possible motive could be mind control. Maybe an enemy manages to take over Kakashi's mind and forces him to harm Naruto. Another could be a misunderstanding. For example, if Naruto was thought to be possessed by a powerful and dangerous entity that Kakashi believed could only be stopped by killing Naruto.
One possible motive could be power. Bowser has always been after power and ruling the Mushroom Kingdom. Maybe in this fanfic, Mario was getting too much influence or was about to discover something that could undermine Bowser's power, so he decided to kill him.
Perhaps in this fanfiction, Jiraiya discovers that Naruto is going to be the cause of a major catastrophe in the future. He might have seen a prophecy or some sort of sign that convinces him Naruto has to die to prevent this. It could also be that Jiraiya has been misled by false information about Naruto, which makes him think that Naruto has become an evil force that needs to be eliminated.
It could be that Yagura had some secret plans that would endanger the balance among the ninja villages. Naruto, having a strong sense of protecting peace, discovers these plans and decides that eliminating Yagura is necessary. For example, if Yagura was planning to use a powerful and dangerous jutsu that could destroy multiple villages, Naruto would act to prevent it even if it means killing him.