Who could be the main antagonist in 'naruto is an ignored prodigy fanfiction'?

The Akatsuki could still be the main antagonists. Since Naruto now has Uchiha powers, they might be even more interested in him. They could see him as a threat or a valuable asset to their plans, just like they did with Sasuke.

One option for the main antagonist could be a secret organization that has infiltrated Konoha. They target the Anbu prodigy because they fear the prodigy's abilities could expose their existence and plans. This organization might have members with unique and dangerous abilities themselves. They would constantly send assassins after the prodigy and try to create chaos in Konoha to keep the Anbu and the prodigy distracted while they carry out their real objectives.

Well, it could be about Naruto being overlooked despite his great potential. Maybe he's constantly underestimated by his peers and even some of his teachers. He might secretly develop amazing skills that no one notices until a crucial moment in a battle or some big event.

Maybe an entire rival village decides to target the prodigy. They see the potential threat that the prodigy poses to their own village's dominance, so they send their best ninjas to take the prodigy down.

It could be someone like Rock Lee. He was a hard - working prodigy in taijutsu, but often got overshadowed by the more flashy abilities of others. Maybe in this fanfiction, he's completely forgotten until he does something extraordinary to get noticed again.

Perhaps it could be a new character created specifically for the fanfiction. A young ninja from a minor clan who showed extraordinary talent in a unique form of jutsu. But because their clan was small and not very influential, and the larger clans felt threatened by this new talent, they managed to get the village to abandon this prodigy.

It could be an original character created by the fanfiction author. This character might have a special background or power that makes them a ninjutsu prodigy.

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.