It could be a rogue ninja who wants to use mokujin's power for his own evil purposes. He might try to control mokujin and use his unique abilities to take over the ninja world.
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.
Maybe the Xenomorph Queen herself could be the main antagonist. She is intelligent and powerful. She sees Naruto's world as a new place to colonize and sends her Xenomorph minions to attack. Naruto has to find a way to stop her before she spreads too many eggs and creates an unstoppable army.
Maybe Danzo. He's always been a power - hungry character. In a story where Naruto doesn't have the jinchuuriki advantage, Danzo could see it as an opportunity to take over the village without the threat of Naruto's special power standing in his way.
It could be a powerful ninja from Naruto's world who wants to use Aela's powers for his own evil plans. Maybe he thinks her abilities can help him conquer all the ninja villages.
It could be an evil elf who has been exiled from their own elven community for practicing dark magic. This elf might see the Ninja world as a place to gain more power and cause chaos. They could target Naruto specifically because they sense his strong chakra and want to either steal it or use him as a tool for their evil plans.