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.
There might be an organization in the fanfiction that exists across multiple dimensions and is dedicated to maintaining the 'balance' in a very cruel and unjust way. They would oppose Naruto and Naruko's attempts to change things for the better in the dimensions they visit, seeing their actions as disrupting the 'natural order' of things.
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 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.
Often, the main antagonists can be the village elders or some corrupt shinobi within the village who are behind their banishment. These characters may fear Naruto and Naruko's growing power and influence.
Well, it could be an ancient being that has been sealed away in a dimension for centuries. Naruto's arrival could break the seal accidentally, and this being, full of anger and a thirst for power, would become the main antagonist. Another option is a self - proclaimed god in a dimension who believes that Naruto's presence is an insult to his divinity. He would then try to eliminate Naruto. There could also be a group of anti - ninja fanatics in a dimension who view Naruto as a symbol of everything they hate about ninjas and would stop at nothing to get rid of him.
It could be Orochimaru. Even though he was defeated before, he might come back with a new plan. Maybe he wants to use Naruto and Naruko's family for some dark experiment, like trying to extract the unique chakra combination that their family might have.
Maybe a new organization of rogue ninjas that see Naruto's Rinnegan as a threat to their own goals of taking over the ninja world. They target Naruko as a way to get to Naruto. These ninjas could have some unique and powerful jutsus of their own, making them formidable antagonists.
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.
It could be a rogue ninja who is jealous of Naruto's godlike powers and wants to take them for himself. This ninja might target Naruko as a way to get to Naruto.
Danzo Shimura might be another one. He is very secretive and power - hungry. If Naruto and Naruko's time - traveling actions expose his dark deeds or interfere with his control over the village, he would become their enemy. He has many underhanded methods and a strong influence within the village that they would have to deal with.
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.