Maybe a powerful rogue ninja who has discovered a way to steal the powers of divine entities. He sets his sights on Amaterasu and Naruto because he knows that if he can combine their powers, he will be unstoppable. He creates various traps and illusions to separate them and weaken them so that he can carry out his evil plan.
It could be a rogue ninja who has also discovered a way to harness the power of Amaterasu in a corrupt way. This ninja might want to use the power to take over the ninja villages and Naruto stands in his way.
There could be a group of ninja from a hidden village that has always been envious of Konoha's power. When they hear about Naruto being blessed by Amaterasu, they see it as an opportunity to weaken Konoha. So, they send their best assassins to either kill Naruto or steal his power, making this group the main antagonists in the fanfiction.
Perhaps a powerful demon that has a grudge against the power of Amaterasu. It targets Naruto because he is the one who seems to be getting closer to Amaterasu. The demon could be from an ancient time when Amaterasu was first used to seal it away, and now it's back to stop Naruto from fully understanding and using Amaterasu.
It could be someone who wants to steal Samehada for its power. Maybe a rogue ninja who has heard of Samehada's ability to absorb chakra and plans to use it to take over the ninja world.
It could be a powerful alchemist who has gone rogue and wants to use Naruto's chakra for some dark alchemy purpose.
Well, perhaps in the fanfiction, Naruto is in a spiritual realm and meets Amaterasu there. Amaterasu could be in trouble, her powers waning due to some dark magic. Naruto, with his never - give - up attitude, decides to help her. He uses his shadow clones to search for the source of the problem while Amaterasu shares some of her ancient wisdom with him. In the end, Naruto manages to restore Amaterasu's power and in return, she bestows upon him a new type of chakra that gives him an edge in his battles back in the real world.
It could be an evil ninja who wants to capture the fem Kyuubi for her power. He might see the unique bond between Naruto and the fem Kyuubi as a threat to his plans of world domination.
Maybe Orochimaru could be the antagonist. He hears about Naruto's encounter with Yagura and wants to use their connection for his own evil experiments. He might try to capture Yagura again (if he was once under Orochimaru's control) or manipulate Naruto into doing something that would harm Yagura and the relationship between the two villages.
It could be someone who doesn't want Naruto and his sister to unite. Maybe a rogue ninja who fears their combined power. He might try to drive a wedge between them by spreading false rumors or causing misunderstandings.
It could be an evil shinobi who wants to disrupt the meeting between Naruto and Kushina. Maybe they know that Kushina has some special knowledge or power that she could pass on to Naruto, and they don't want that to happen.