One possibility is that Naruto and Naruko are on a mission to save the multiverse in this fanfiction. They travel through dimensions to collect some special artifacts or powers that are scattered across different realities. Along the way, they might face challenges from the rulers of those dimensions who don't want them to take those things. This could involve epic battles and the forging of new alliances as they strive to complete their mission.
It could be some powerful dimension - hopping villains who want to use the power of different dimensions for their own evil purposes. They might see Naruto and Naruko as threats to their plans.
One potential antagonist could be a rogue ninja from another dimension who wants to use Naruto and Naruko's abilities for his own gain. He might be jealous of their power and try to trap them in different dimensions to study their techniques. Another could be a powerful entity that controls the portals between dimensions and doesn't want Naruto and Naruko messing around with the balance of different worlds.
One possible plot could be that Naruto and Naruko accidentally stumble upon a powerful jutsu or a strange artifact that opens a portal to different dimensions. In each dimension, they face unique challenges. For example, in a dimension where ninjas have different powers, they might have to learn new fighting styles to survive. They could also meet alternate versions of their friends and enemies, which would lead to interesting interactions and character development.
He often meets versions of himself from different dimensions. These other Narutos might have different personalities or abilities due to the differences in their respective dimensions.
Perhaps Naruto travels to a dimension where everyone has a unique animal spirit companion. He has to bond with one of these spirits to gain access to certain powers. This would be a whole new experience for him as he's used to his own ninja world and its rules.
Well, he might visit the dimension of the Sharingan's origin, where he could learn more about the Uchiha clan's secrets. Another could be a dimension full of powerful beasts, much stronger than the tailed beasts in his own world. And there could also be a dimension of pure chakra, where he can train and enhance his chakra control to an extreme level.
Kakashi could also be a character in 'naruto and naruko harem fanfiction'. He can be the mentor figure, guiding Naruto and Naruko through different situations. His wisdom can influence how the harem relationships develop, for example, by giving Naruto advice on how to handle multiple relationships in a proper way.
In this fanfiction, Naruto and Naruko's characters can be developed through their shared experiences. They could face discrimination or special treatment because they are twins. Naruto, who is used to being an outcast, might handle it one way, while Naruko could have a different reaction. This would lead to them growing as individuals and as a pair. They could also develop by learning from each other's mistakes. For instance, if Naruto rushes into a fight, Naruko could teach him the value of planning, and Naruto could show her the importance of believing in oneself no matter what.