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.
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.
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.
One great anime is 'Sword Art Online'. The main character, Kirito, is extremely overpowered (OP). He is highly skilled in the virtual reality world of SAO. In the series, he also has a love story with Asuna. Their relationship develops as they face various challenges together in the dangerous game world.
In such a fanfiction, Allen might become a much darker character. He could start to use his powers without any moral restraint. For example, he might not care about innocent bystanders while fighting the Akuma. His relationships with his friends in the Black Order would also be severely strained. They would be shocked and probably try to bring him back to his former self, but it would be a difficult and dangerous process.
One good anime is 'Sword Art Online'. The main character, Kirito, is extremely overpowered. He's highly skilled in combat within the virtual world of SAO. And there's a love story between him and Asuna. Their relationship develops as they face various challenges in the game world.
Itachi might be involved. Even though he has his own complex backstory, in this fanfiction, his powerful abilities and knowledge could be used to try and stop Naruto from losing his humanity completely. And the yaoi aspect could come in as Itachi forms a deep, perhaps unorthodox bond with Naruto during this process. Another character could be Neji. He has always been somewhat of a rival and friend to Naruto. Here, he could be the one who is determined to bring Naruto back to his normal self, and a yaoi - themed relationship could potentially develop between them as Neji delves deeper into Naruto's situation.
The plot could develop with Allen becoming a new antagonist. He starts causing chaos and destruction, and the Black Order has to find a way to stop him. Maybe they try to find a way to restore his humanity, but it's not easy as they also have to deal with other threats in the world of D Gray - Man.
Fullmetal Alchemist: Brotherhood. Edward Elric is a very capable alchemist. The story is about the brothers' journey to find the Philosopher's Stone to restore their bodies. It has a great blend of action, mystery, and moral lessons, with a well - crafted world and engaging characters.