In some cases, it could be Naruto's own inner demons. He has been through so much in his life, and all the traumas and pressures he has faced could manifest as fear within him. Maybe in the fanfic, his past experiences resurface and become the source of his fear.
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.
One reason could be a past bad experience. Maybe he had a really painful treatment as a kid that left a deep mark. For example, if he had a serious injury once and the doctor was rough while treating him, it would make him fear doctors.
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.
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.
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 a new villain. Maybe a villain who targets Naruto's loved ones and Naruto is unable to save them. This failure would cause him great heartbreak. For instance, if the villain kidnapped Hinata and Naruto couldn't rescue her in time.
One possible reason could be that his sister has some special or unknown powers that Naruto doesn't understand. For example, if she has a very unpredictable and potentially dangerous kekkei genkai. Another reason might be that she has a very strong and intimidating personality, which makes Naruto feel small and scared in her presence.
A new, powerful and arrogant villain introduced in the fanfic could be the cause. This villain could constantly mock Naruto and his ideals, and try to undermine his efforts to protect the village. Such blatant disrespect would make Naruto really pissed off as he is very protective of his home and the values he stands for.
One possible reason could be that they had a past traumatic experience related to explosions. Maybe they witnessed an explosion that caused harm to their loved ones or themselves. Another reason might be that explosions in the 'Naruto' world are often associated with powerful and dangerous jutsus or attacks, and they are simply afraid of the destruction and chaos that explosions can bring.
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.