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.
The disowning could also have an impact on the other characters. For instance, Hinata might be caught in the middle, trying to reconcile Naruto and Boruto. The other villagers might have different opinions about the situation. Some might side with Naruto, believing he had a good reason, while others might think Naruto is being too harsh on Boruto. This can add layers of complexity to the fanfiction's plot.
Naruto might be extremely heartbroken. He has always looked up to his mother, and being disowned by her would be a huge blow. He could become withdrawn and start to question his own worth.
Physically, Naruto can use his Rasengan or other powerful jutsus to fend off enemies attacking Boruto. His combat skills are top - notch, and he won't hesitate to engage in battle to keep Boruto safe.
It could be due to a perceived betrayal. Suppose Naruto discovers some dark secrets within his family that he can't overlook. In his 'godlike' state, he might be more morally rigid and thus decides to disown them. For instance, if he finds out that his family was involved in some unethical ninja practices in the past, he would feel compelled to distance himself.
It could also be due to some external influence. Perhaps an enemy used some kind of mind - control or manipulation on Kushina. They made her think that Naruto was a threat, so she decided to disown him. In the Naruto universe, there are many powerful villains who could potentially do this kind of thing.
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.
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.
They could start by having an honest conversation. Naruto could sit down with Boruto and just listen to his fears without judgment. This would be a first step in building a better relationship.
One great 'Boruto and Naruto Fanfiction' is 'A New Era of Shinobi'. It really delves into how Boruto and Naruto's relationship could evolve further, with Boruto learning new jutsus from his father in a more in - depth way than in the canon story. It also explores the political unrest in the shinobi world that wasn't fully covered in the anime or manga.