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.
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.
A 'Naruto loses his memory fanfiction' might involve a mysterious curse placed on Naruto. He forgets not only his personal relationships but also his ninja skills. His sensei, Kakashi, could take it upon himself to reteach Naruto everything from the basics. Meanwhile, Naruto might form new, unexpected relationships with people in the village who don't know the 'old' him, and these new relationships could either help or hinder his journey to regain his memory.
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.
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 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.
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.
One possible reason could be for Naruto's protection. His parents might think that by giving away his birthright, they can keep him away from dangerous enemies or political intrigue in the ninja world. Maybe they foresee a great threat that would target Naruto specifically because of his birthright, and this is their extreme measure to ensure his survival.
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.