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.
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.
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.
Iruka - sensei could be one of those who help Naruto. He has always been like a father figure to Naruto and would offer emotional support. Rock Lee could also be a great helper. Lee, who has trained his body to be extremely powerful, could teach Naruto some physical combat techniques that don't rely on eyesight. And of course, the Nine - Tails inside Naruto might also play a role. It could potentially share some of its power or knowledge to help Naruto deal with his new situation.
One possible consequence could be a change in his fighting style. Without his eye, he might have to rely more on his other senses like hearing and smell, similar to how blind ninja in the Naruto universe adapt. For example, he could focus more on using his chakra to sense the movements of his opponents.
Naruto might also go through an identity crisis. His whole life has been centered around being a ninja with chakra and using powerful jutsu. Losing his chakra could make him question who he is and what his purpose is. He would have to redefine himself and find a new way to contribute to the ninja world. This could be a long and difficult process for him.