Another antagonist could be an organization that views the Rinnegan as a dangerous power that needs to be controlled or destroyed. They might target Naruto not just because of the Rinnegan but also because of his status as a hero in the ninja world. This would put Naruto in a difficult position as he has to fight against an entire group while also trying to understand their motives.
One possible antagonist could be a rogue ninja who also wants the power of the Rinnegan. He might see Naruto as a target to either steal the power from or eliminate so that he can be the most powerful in the ninja world. This character could be a new creation or an existing villain with a new motivation.
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.
A new character could be introduced as the main antagonist. This character could be an outcast ninja who has secretly been researching and combining the powers of EMS and Rinnegan. He believes that the ninja world should be ruled by the strongest, and he thinks he is the one. So he starts causing chaos and destruction, and Naruto has to stop him using his own EMS - Rinnegan combination.
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.
In the RWBY world, Salem could be a major antagonist. She might view Naruto's son as a threat to her plans for Remnant. His unique powers and knowledge from the ninja world could potentially disrupt her schemes, so she would try to eliminate him.
One potential antagonist could be Orochimaru. He is always after powerful jutsus and the power of the Rinnegan would be extremely appealing to him. He might try to either steal Naruto's newly awakened Rinnegan or prevent Naruto from fully mastering it so that he can be the most powerful one in the ninja world.
There could also be new characters introduced as antagonists. In this fanfiction, perhaps there are dark entities that are either drawn to Naruto's new evil self or are competing with him for control. They might have powers that rival or complement his Rinnegan - based abilities, leading to some intense battles and power struggles.
The main antagonists could be members of an ancient clan who see Naruto's emerging powers from his bloodline as a threat to their own plans for power. They might fear that his newfound abilities will disrupt the balance of power they have been carefully cultivating for generations.
The Akatsuki as a whole could be antagonists. In fanfictions, the Akatsuki might be interested in the power of Naruto's Evil Rinnegan. They could try to capture him to extract the power or use him in some way for their own goals. Pain, being a powerful member of the Akatsuki, could also be a specific antagonist. His own ideology about pain and peace might clash with Naruto's new, potentially more chaotic state with the Evil Rinnegan. Additionally, new original antagonists created specifically for the fanfiction could be common. These could be dark, powerful figures who are drawn to the power of the Evil Rinnegan and want to either possess it or destroy Naruto to prevent its misuse.
The old shinobi council from his former village could be antagonists. They might still see Naruto as a threat even in exile and try to harm his kids to prevent them from becoming powerful. Or perhaps some new villains who want to use Naruto's kids to get to him, knowing his strong bond with them.
The Sound Ninjas could be great antagonists. They could use their own unique parkour - like skills to try and stop Naruto. They might be chasing him through the forest, and Naruto has to use his parkour skills to outmaneuver them.