Another interesting angle could be that the devil gene was secretly implanted in Naruto by an enemy. As he grows, the gene starts to manifest and the village begins to fear him. Naruto then has to prove that he's still the same person and that he can use this new power to protect the village, not destroy it.
Maybe in the fanfiction, the devil gene is linked to an ancient curse in the Naruto universe. Naruto has to go on a journey to find out the origin of this gene and how to either get rid of it or use it for good. He could meet some new characters who are also affected by similar genes and they form an unlikely alliance.
One idea could be a story where Naruto discovers he has a devil gene that gives him new and dark powers. He struggles to control these powers while still maintaining his values. For example, the devil gene might make his shadow clones more menacing and powerful, but they also start to have a mind of their own.