A new, unknown villain could be the cause. This villain might have a special power related to mind control or mental manipulation. They target Naruto because of his status as a hero in the ninja world. By making Naruto lose his mind, they could throw the entire ninja world into chaos.
It could be Orochimaru. He is known for his devious ways and might manipulate Naruto into believing false things about the ninja world.
In this fanfiction, there could be a villain who has the ability to manipulate Naruto's mind. The villain might use this power to make Naruto turn against the Hidden Leaf Village. Naruto, without control of his own mind, could start causing chaos within the village, like attacking important buildings or trying to steal important ninja secrets.
Perhaps it's an old enemy that was thought to be defeated. This enemy might have been biding their time and finally finds a way to get revenge on Harry by driving him mad. It could be a Death Eater who was overlooked or a creature from the Forbidden Forest with a grudge.
Well, he could start making really rash decisions. Maybe he'd attack his friends by mistake, thinking they were enemies. Since he's lost his mind, his usual judgment would be out the window.
There's also the possibility that it's an accidental injury caused by one of Naruto's friends during a training session gone wrong. For example, Sasuke could accidentally unleash a jutsu that hits Naruto's eye while they are sparring.
It could be Sasuke. If Sasuke has some sort of newfound connection with Naruto and it causes Naruto to shift his focus away from Sakura, then Sasuke would be the cause. For example, if Sasuke and Naruto team up for a powerful mission and their bond deepens in a way that makes Naruto neglect his relationship with Sakura.
It could be Danzo. He was always power - hungry and had his own ideas about what was best for the village. He might see Naruto as a threat and find a way to take away his birthright.
Perhaps he was in a battle against a very strong enemy. The enemy might have used a special attack that specifically targeted his eyes, like a genjutsu that damaged his optic nerves when he broke free from it.
In this fanfiction, it could be that the pressure of being 'The Chosen One' finally gets to Harry. All the battles, the losses he has endured, and the constant threat of Voldemort might push him over the edge. He could start acting erratically, pushing away his friends and allies because he no longer trusts his own judgment.
Arthur could be the cause. He often bosses Merlin around and doesn't fully understand Merlin's capabilities. His constant demands and lack of respect for Merlin's intelligence might push Merlin to the edge. For instance, when Arthur makes Merlin do dangerous and pointless tasks without any regard for his safety.