Perhaps a new group of rogue ninja who are jealous of Naruto's new power. They might want to steal the power of the wolf - bijuu from Naruto to gain dominance in the ninja world. They could be led by a powerful and vengeful ninja who has a personal grudge against Naruto or the Hidden Leaf Village.
It could be Orochimaru. He's always interested in strange and powerful forms, and Naruto's new wolf - bijuu form would be something he'd want to study or even control for his own evil purposes.
The Akatsuki might be the main antagonists. Since Naruto has become a wolf - bijuu, they would see him as an even greater threat or a valuable asset to capture. They might send their most powerful members like Itachi or Pain to hunt him down.
The Akatsuki could also be the main antagonists. Since they are after the bijuu, they would surely target Naruto once he has this special relationship with them. They might try more elaborate schemes to capture the bijuu from Naruto and his 'harem' of sorts.
Maybe there is an ancient wolf demon spirit that is corrupted and sees Naruto as a threat to its reign. This spirit would try to either kill Naruto or corrupt him further, causing chaos in the world.
The Akatsuki might also be the main antagonists. They were after the bijuu in the original story. With Naruto having two, they would surely target him. They might see it as an opportunity to gain an even greater edge in their plan to control the world.
Well, perhaps in the 'naruto becomes a wolf bijuu fanfiction', Naruto is transformed into a wolf - like Bijuu form due to some dark magic or a strange experiment gone wrong. His friends initially don't recognize him, and he has to struggle to control this new form while also trying to show them it's still him. He may learn new jutsus that are unique to this wolf - bijuu form and use them to protect the village from new threats that are too powerful for his normal form.
Maybe there's a rogue ninja who has developed a new and dangerous jutsu that can counter Naruto's powers. This ninja wants to prove himself as the strongest by defeating Naruto and taking over the bijuu's power. He might be jealous of Naruto's newfound status and the respect he gets from the other ninjas.
The Hidden Leaf Village elders could be main antagonists. If Naruto turns dark because he feels betrayed by the village, they would be the ones representing the establishment he is against. Their conservative and sometimes self - serving ways could be the catalyst for Naruto's transformation, and then they would be the ones trying to stop him as he becomes a threat to their power and the village's traditional order.
The Hidden Leaf Village elders could be antagonists. If Naruto turns dark, they might see him as a threat to their power and try to stop him. Their actions against Naruto could further fuel his descent into darkness.
The Hidden Leaf Village itself could become the main antagonist. Since Naruto turns evil, the village that once nurtured him would now be against him. The village elders and some of the ninja who oppose Naruto's new evil ways would be in conflict with him. For example, Kakashi might be forced to fight against Naruto to protect the village.
The main antagonists could be the ones who banished Naruto in the first place. Maybe it was a group of elders in the village who feared Naruto's power and wanted to get rid of him. They would see Naruto as a threat now that he is becoming the Onikage and would try to stop him from returning to the village or causing any changes.
Perhaps it's a jealous ninja from another village. This ninja has always been envious of Naruto's power. So when he gets the chance, he uses a dark magic to turn Naruto into a wolf. His goal is to make Naruto weak and lose his status among the ninja community.