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.
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.
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.
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.
The village elders might see Naruto's memory loss as a threat to the village if they think it affects his ability to protect it. They could try to keep an eye on Naruto and the male character he is involved with in the Yaoi relationship. This could create tension as the two just want to figure out Naruto's situation and develop their relationship, but now they have to deal with the watchful eyes of the elders.
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.
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.