One possibility could be that Jiraiya is under the influence of a powerful enemy's jutsu that makes him lose control of his actions and accidentally attacks Naruto. This could lead to a great deal of guilt and self - loathing for Jiraiya later.
I'm not aware of a common 'naruto kills jiraiya fanfic'. In the original Naruto series, Naruto respects Jiraiya deeply. Such a plot would be a huge deviation from the canon and go against Naruto's character. It's hard to imagine a legitimate story where Naruto would kill Jiraiya.
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 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.
The impact would be significant. Since Naruto has such a large and passionate fandom, this fanfiction would be like a bomb. Some fans would stop reading fanfictions altogether if they find this concept too disturbing. Others might start creating counter - fanfictions where they try to rewrite the scenario to something more in line with the original spirit of the series. It could also lead to a decrease in the popularity of the overall fanfiction community related to Naruto if this kind of extreme and negative content becomes more common.
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 wants to explore his own path independently and test his skills without Jiraiya's constant guidance.
A fanfic like this might explore how fem Naruto's presence affects Jiraiya's typical behavior. Jiraiya is known for his pervy tendencies in the original series, but with a fem Naruto, he might have to control himself more. It could also be about how fem Naruto looks up to Jiraiya as a strong ninja and a source of wisdom, and how she tries to learn from him to become a great kunoichi.
One great Jiraiya and Naruto fanfic is 'The Mentor's Legacy'. It delves deep into how Jiraiya's teachings continue to influence Naruto even after his death. It has some really heart - warming moments where Naruto reflects on their time together and uses Jiraiya's wisdom in his battles.