Well, it could be due to a plot twist in the fanfiction. The author might want to show Naruto's growth in a more extreme way. Naruto could have received some special training from an unknown source that gives him an edge over Neji. He might also be under the influence of a special power - up item or a curse that enhances his abilities but also makes him more violent. In that case, his strength could easily overpower Neji's skills.
Perhaps in the fanfiction's universe, Neji has some sort of weakness that Naruto exploits. Maybe Neji has an injury from a previous battle that he hasn't fully recovered from, and Naruto takes advantage of this. Or it could be that Naruto has formed an alliance with other powerful characters who help him take down Neji. For instance, if Naruto teams up with Sasuke, who has his own set of powerful jutsus, they could easily overpower Neji.
In a fanfiction where Naruto destroys Marineford, it could be due to his overpowered jutsu. Maybe he uses his Rasengan in a super - enhanced form that creates a massive explosion, leveling the Marineford. Another possibility is that he uses his Sage Mode to outmaneuver all the opponents there and then unleash a devastating attack.
In the Naruto universe, Naruto killing Neji would be a very dark and out - of - character turn. However, in fanfiction, it could be due to some dark influence like a powerful and evil genjutsu that overpowers Naruto's mind and makes him see Neji as an enemy. Maybe a villain has managed to manipulate Naruto's perception of reality to make him commit such an act.
Jealousy could be a reason. Suppose Neji has achieved something that Naruto desperately wants, like a high - ranking position in the village or a special recognition. Naruto's envy could turn into anger and fuel a fight where he overpowers Neji. Another reason could be a misunderstanding. Maybe Neji is wrongly accused of something that Naruto holds dear, like endangering a friend. Naruto, in his haste to protect and seek justice, attacks Neji with full force.
One possible plotline could be that Naruto has a sudden and extreme power-up that makes him overconfident. This overconfidence leads him to challenge Neji in a spar that gets out of hand and he ends up 'destroying' Neji in the sense of completely overpowering him. Maybe Naruto has unlocked a new form of his chakra that Neji can't counter with his Gentle Fist technique.
Perhaps in this fanfiction, Neji is brought back to life somehow. Boruto, being curious, approaches Neji. Neji then discovers how much the ninja world has changed since his time. Boruto could show Neji the new technology in the Hidden Leaf Village. Neji might be a bit shocked at first but then start to see the potential in these new things. They could also form an unlikely friendship, with Neji guiding Boruto in matters of honor and discipline, which are values Neji held dear.
In such a fanfiction, it would be a very dark and alternative take. Naruto, being godlike, might have been pushed to the edge by something in Konoha, like betrayal or unjust treatment. Maybe he discovers some dark secrets about the village leaders that make him snap.
He could realize his mistake later on. Maybe he has a moment of clarity where he remembers the true nature of his family and how much they love him. He then uses his strong willpower to fight against whatever was controlling him before and tries to make amends.
It could be Sasuke. If he were to turn to the dark side in the fanfiction, his Rinnegan powers could be used to destroy Konoha. He has the potential to be extremely powerful and if he has some sort of vendetta or is influenced by some dark force, he might take his anger out on the village.
Madara Uchiha could also be a possible antagonist in this scenario. Even if he is dead in the original story, in a fanfiction, his lingering influence or a resurrected form could manipulate Naruto. Madara was always against Konoha's ideals to some extent and might use Naruto as a tool to destroy what he hated.
One possibility could be that Naruto is somehow transported to the world of Greek mythology where Olympus exists. Maybe his powerful jutsu are seen as a threat to the gods on Olympus. He could start by accidentally causing chaos in a nearby village which gets the attention of the minor gods. As they try to stop him, he realizes he has to fight back to protect himself and in the process, his attacks end up targeting Olympus.