It could be that Naruto witnesses something so horrible that it breaks his spirit and makes him lose his humanity. For instance, if all his friends were killed in front of him in a brutal way and he blames himself. This could drive him into a dark state where he becomes cold - hearted, seeing the world only as a place of pain and vengeance, and his actions would no longer be guided by the positive values he once held.
Maybe he loses his humanity as a result of a failed experiment. Some rogue ninja or a secret organization might try to enhance his power but end up corrupting his very essence. As a consequence, Naruto could start to show no mercy, lack empathy, and use his powers for destruction rather than protection.
In such a fanfiction, one possible plot could be that Naruto is exposed to some dark magic or a powerful curse that gradually erodes his humanity. This might lead to him becoming cold and detached from his friends. He could start making decisions that go against his normal moral code, perhaps being more ruthless in battle or in his relationships. The yaoi aspect might come into play if another male character tries to bring back his humanity through a deep emotional and physical connection with Naruto.
A new and mysterious dark ninja could be the main antagonist. This character might have a special ability to corrupt others. They target Naruto specifically because of his power and influence. By using some form of dark jutsu or psychological manipulation, they make Naruto lose his humanity, turning him into a weapon against the very people he used to protect.
In such a scenario, his relationships would be severely affected. His friends would be horrified by the change in him. Naruto's bond with Sasuke, for example, would be in jeopardy. Since he has lost his humanity, he may not understand the concept of friendship anymore and might even see Sasuke as a rival to be eliminated. And his relationship with the female Kyuubi would be complex. Maybe she would try to control him or use his new state for her own purposes.
Maybe Orochimaru manages to get his hands on Naruto and subjects him to some dark and twisted experiments. These experiments could mess with Naruto's mind, causing him to lose his sanity. He could start seeing illusions all the time, believing his friends are his enemies. As a result, he'd be in a constant state of confusion and aggression, and his once - positive attitude towards life and ninja - hood would be completely gone.
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.
In such a fanfiction, perhaps Naruto could be wrongly accused of something that leads to him being stripped of his birthright. Maybe a false claim about his connection to the Nine - Tails is used against him.
Well, one possible plot could be that Naruto is cursed by an enemy during a battle. This curse takes away his voice. As a result, he has to find new ways to communicate with his friends and allies. Maybe he starts using sign language, which he has to learn quickly. This could lead to some really interesting character development as he struggles to convey his thoughts and emotions without speaking.
One possible plot could be that Naruto is put under a powerful genjutsu. This genjutsu messes with his mind and slowly drains his emotions. As a result, he becomes detached from his friends and his sense of purpose. He no longer shows excitement for training or fighting, and his usual determination fades away.
In this fanfiction, it could be that Naruto's left - eye loss is part of a curse placed on him by an ancient evil. This curse not only takes his eye but also starts to drain his chakra. Naruto then has to search for the origin of the curse to break it. Along the way, he meets some new characters who either help or hinder him. His relationship with Sasuke could also be affected as Sasuke might see Naruto as weakened and try to protect him in his own way, which Naruto would initially resist as he doesn't want to be seen as a liability.
The plot could also involve Naruto's memory loss being a result of some sort of dark magic or curse. And the male character in the Yaoi relationship has to go on a journey to find a way to restore Naruto's memories. During this journey, they grow closer and their relationship deepens in ways it wouldn't have if Naruto hadn't lost his memories. Their shared experiences during this time create a stronger emotional bond between them.