Perhaps an ancient Uchiha clan member whose soul was wronged in the past. Since the Uchiha have a lot of dark secrets, their grudge could target Naruto for some reason. It could be related to the Sharingan or some long - forgotten Uchiha feud.
The Akatsuki members' collective negative energy could be the cause. Even after their defeat, the combined malice and dark intentions they had during their lifetime might manifest as a haunting force that targets Naruto, as he was one of the main opponents of the Akatsuki.
A Naruto fanfic can be for a good cause if it promotes positive values like friendship, just like how Naruto values his friends. For example, a fanfic could show characters from different villages coming together to help each other in a time of crisis.
Maybe Naruto gets cursed during a mission, and the curse makes him see apparitions of his worst fears. These apparitions haunt him everywhere he goes. For example, he might see the ghosts of his fallen comrades or the villains he thought he had defeated, and he has to find a way to break the curse.
One common element is the spooky atmosphere. There are usually things like creaking floors, cold drafts, and strange noises to set the mood. Another element is the use of Naruto's ninja abilities in a new and different context. Since it's a haunted mansion, he might use his shadow clone jutsu to scout ahead or his rasengan to break through barriers created by the haunted forces.
Maybe he has been through some extremely traumatic event. For instance, if he lost all his friends in a single battle, it could be so overwhelming that he shuts down his emotions to cope.
One reason could be false accusations. If Naruto is wrongly accused of a major crime in the village and no one believes him, he might start to hate Konoha.
It could be an old enemy who has come back with new and more terrifying powers. For instance, Orochimaru might return with some kind of jutsu that can directly target Naruto's mind and create unfathomable fears in him.
In some cases, it could be a new and powerful enemy. This enemy might have the ability to manipulate chakra in a way that affects Naruto's mind. For example, they could send out waves of negative chakra that slowly erode Naruto's mental state. Over time, these attacks make Naruto go insane as he struggles to fight against this unseen and insidious force.
Madara Uchiha could be the cause. Even if he's dead, his influence could still be around. Maybe he left behind some sort of genjutsu or curse that affects Naruto's mind and drives him crazy. After all, Madara was always planning something big and Naruto would be a great pawn if he's out of control.
It could be Orochimaru. He's always been interested in Naruto's power. He might use some new jutsu or experiment on Naruto to make him go berserk so he can study his power in that state.