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.
Jiraiya himself would be completely broken. He was Naruto's mentor and had high hopes for him. His actions would likely make him an outcast in the village. Also, the Nine - Tails within Naruto would be a major factor. Its power might go out of control or be lost forever, which could have unforeseen consequences for the balance of power in the Naruto universe.
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.
Sakura would be heartbroken. She had grown up with Naruto and always saw his potential. His death would make her question a lot of things. She might become more withdrawn and serious, vowing to become stronger in Naruto's memory. Kakashi would be deeply saddened as well. He had trained Naruto and seen his growth. He would likely feel responsible in some way too, as he was one of Naruto's teachers. As for Hinata, she would be shattered. She had deep feelings for Naruto, and his death would be almost unbearable for her. She might become more determined to protect the village in Naruto's name.
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.