Madara Uchiha could also be a potential antagonist in this fanfiction. If he somehow returns or has some sort of lingering influence, he might see the bond between Naruto and the Rookie 9 as a threat to his plans. So, he uses his power or some sort of jutsu to make Naruto ignore his friends, with the intention of weakening the village's unity.
Maybe a new, original character created for this fanfiction could be the main antagonist. This character could be jealous of the Rookie 9's friendship with Naruto and use some dark magic or special ability to make Naruto ignore them. The new character's motives could be centered around wanting Naruto's power or attention all for themselves.
It could be Orochimaru. He's always been interested in Naruto and might come up with a plan to drive a wedge between Naruto and the Rookie 9. By making Naruto ignore them, he could be trying to isolate Naruto and make him more vulnerable to his attacks or manipulations.
Perhaps an outsider from a far - off land. This antagonist could be part of a group that wants to disrupt the balance of power in the ninja world by eliminating the potential of the rookies in Konoha. They see Naruto and his fellow rookies as a threat to their future plans.
The plot might involve Naruto being influenced by some external force. For example, a new enemy could be using some kind of mind - control or illusion on him to make him ignore the Rookie 9. Another possibility is that Naruto has become so focused on his training to become stronger that he starts to neglect his relationships with the Rookie 9, thinking that his power is more important for the future of the village.
It could be a new, mysterious ninja from a far - off land. This ninja has some sort of mind - control ability and is using it on Naruto to make him ignore everyone. The antagonist's goal might be to weaken the Hidden Leaf village by causing internal chaos through Naruto's isolation.
It could be the person who spreads false rumors about Jiraiya to Naruto. This person might be an enemy of Jiraiya who wants to drive a wedge between him and Naruto. By making Naruto ignore Jiraiya, they hope to weaken both of them.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.
It could be a corrupt ninja from within the village who wants Naruto out of the way. Maybe someone jealous of Naruto's popularity and power, so they frame him and get him sent to prison. This antagonist would then try to keep Naruto in prison by any means necessary.
Madara Uchiha could be a great antagonist. His powerful Sharingan abilities and his grand plans for the Naruto world would put him at odds with Supergirl. He might see her as a threat to his control and try to manipulate or defeat her. Another option could be Kaguya Otsutsuki. Her god - like powers and desire to reshape the world would clash with Supergirl's values and her attempts to protect the people of the Naruto universe.
Maybe it's a ninja who has also been affected by Anodite magic but has turned to the dark side. This ninja could be jealous of Naruto's new powers and want to take them for himself. He would use his knowledge of both ninja techniques and Anodite powers to try and defeat Naruto.
It could be Orochimaru. He's always been interested in immortality and reanimation techniques. Maybe he reanimates Naruto for some evil purpose, like using Naruto's power to take over the ninja world.