Some fanfictions might explore the idea of Naruto being betrayed by someone close to him. This betrayal could lead to a situation where he is caught off - guard and killed. It adds a dark and dramatic twist to the story.
Perhaps in fanfiction, Boruto is associated with a group or ideology that Naruto opposes. This could cause Naruto to view Boruto unfavorably. Also, if there are false rumors or misinformation spread in the fanfiction world about Boruto, Naruto might believe them and start to hate Boruto until the truth is revealed. And sometimes, it's just a way for the writer to make an interesting and unexpected plot twist.
One possible plotline could be a powerful new enemy emerging that neither Naruto nor Boruto can defeat alone. Maybe an ancient evil that has been awakened and has powers far beyond what the ninja world has ever faced. Their deaths could be a sacrifice to seal this evil away, protecting the village and the world at large.
Maybe it's the high expectations that Naruto has for Boruto. Naruto is a hero, and he might unknowingly put a lot of pressure on Boruto to follow in his footsteps. Boruto could be scared of not being able to meet those expectations.
He could be curious about how other fans perceive the events in Naruto Shippuden. Fanfictions can offer unique interpretations and perspectives that might give him new insights.
One possible reason could be that the Kyuubi's power goes out of control completely. Since Naruto has the Kyuubi inside him, if he fails to maintain the balance, the Kyuubi's raw and unrestrained power might end up killing him.
One possible reason could be that she sacrifices herself to save Naruto from a powerful enemy. In the heat of battle, she might put herself in harm's way to ensure Naruto's survival.
Perhaps there was a curse or a disease that he couldn't overcome. In some fanfictions, they like to introduce unique and deadly diseases that not even the best medical ninja can cure. It could also be due to a failed mission where he was caught in a trap that was impossible to escape from, leading to his death.
It could be that the fanfiction simply doesn't meet Boruto's standards for what the Naruto universe should be like. He has grown up in that world and has his own ideas about how things should be. Fanfiction can be very hit - or - miss in terms of quality and faithfulness to the source material. If it's of poor quality or changes things too much, Boruto might hate it.
One reason could be Boruto's recklessness. In fanfiction, Boruto might engage in dangerous stunts or actions that go against Naruto's teachings. For example, if Boruto were to use a forbidden jutsu without fully understanding the consequences, Naruto would be angry as it not only endangers Boruto but also those around him.
It could also be due to a rift in their relationship over Boruto's ninja path. If Boruto decides to take a very different and unorthodox approach to being a ninja that Naruto doesn't approve of, such as using forbidden jutsu without proper understanding, Naruto might disown him in the fanfiction.