In some fanfictions, the writer likes to explore extreme and dark scenarios. So it could be that Jiraiya has his own personal demons and issues. He might have a moral conflict within himself and somehow comes to the conclusion that killing Naruto is the solution. For example, if Jiraiya believes that Naruto's power is too dangerous and uncontrollable, and no other options are available to stop him from causing chaos, he may take the drastic step of killing 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.
There could be a 'naruto kills jiraiya fanfiction'. It could be based on a time - travel scenario. For example, if Naruto from the future travels back in time and somehow his actions cause a chain of events that lead to Jiraiya's death. Or perhaps there's a dark, alternate universe where Naruto's values are twisted and he sees Jiraiya as an obstacle to his new, malevolent goals and thus kills him.
One possible reason could be that Naruto feels he has learned all he can from Jiraiya at that point. Maybe he has reached a level in his training where he believes he needs new experiences and challenges that Jiraiya can no longer provide.
It would be quite a shock to the Naruto fandom. Jiraiya is a beloved character and Naruto is the protagonist. For some fans, it would be a very dark and disturbing concept. It might make some fans angry as it goes against the typical relationship and character development in the original series.
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.
In the 'boruto kills naruto fanfiction', a motive could be a power struggle. Boruto might believe that Naruto's power is holding back the village's growth or his own potential. He could think that by eliminating Naruto, he can bring about a new era of power in the Hidden Leaf. Also, it could be out of desperation. If Boruto is in a situation where he believes that killing Naruto is the only way to save someone he loves, like his mother or a friend, he might take such a drastic step.
One possible motive could be a misunderstanding. Maybe Hiashi mistakes Naruto for an enemy who has infiltrated the village in disguise. Another reason could be related to clan politics. If Naruto somehow gets involved in a situation that threatens Hiashi's clan interests, Hiashi might take extreme measures.
One possible motive could be that Kakuza has committed some heinous crimes against the Hidden Leaf Village. Maybe he has been involved in secret attacks on the village or has been plotting something really bad that would endanger the lives of many villagers. Naruto, being the protector of the village, would then take it upon himself to stop Kakuza by any means necessary, which unfortunately might end up in killing him.
Perhaps Jiraiya has some personal issues or inner conflicts. He might be dealing with his own past traumas or demons that prevent him from taking on the role of Naruto's trainer. For example, he could be haunted by the failures in his previous relationships or battles, and he feels unfit to train Naruto until he sorts out his own problems.
One possible reason could be mind control. Some dark power might take over Naruto's mind and force him to turn on Jiraiya without his own will.
Another reason could be that Jiraiya has some doubts about Naruto's readiness or potential. He might think that Naruto is not yet at the level where he can fully benefit from Jiraiya's training. For example, Naruto may lack some basic skills or knowledge that Jiraiya believes are necessary prerequisites for his more advanced training.