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.
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.
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.
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.
One option could be Kaguya from the Naruto universe. Her god - like powers would pose a great threat to Bayonetta. She could be trying to expand her influence into Bayonetta's world, seeing it as a new place to conquer.
It could be a dark wizard who wants to capture the nymph for her powers. He sees the nymph's connection to nature and wants to use it to gain ultimate power in the Naruto world.
It could be an evil ninja from Naruto's world who has somehow gained the ability to control Digimon. He wants to use this power to rule over both worlds. He targets Renamon because of her connection to Naruto and tries to break their bond. He might also be after the special powers that Naruto and Renamon possess when they work together.
It could be a rogue ninja who has a vendetta against Naruto and sees Heather as a way to get to him. Maybe this ninja was once defeated by Naruto and now wants to use Heather as bait or hurt her to break Naruto's spirit.
Perhaps a rogue ninja who has learned about the mummy's existence and wants to sell it to the highest bidder. He will stop at nothing to get the mummy, even if it means fighting Naruto and causing chaos in the process.
The Akatsuki could also serve as the main antagonists. They might view Naruto and Midnight as threats to their plans. For instance, if they find out that Midnight has some knowledge or power that could disrupt their collection of tailed beasts, they would target them. Naruto and Midnight would then have to fight against the Akatsuki's various members, each with their own dangerous abilities.
It could be a powerful dark wizard from the Enchantress' world who follows her to the Naruto universe. He wants to capture the Enchantress and use her powers for his evil plans, and also sees the chakra in Naruto's world as a new source of power to conquer. He could have dark magic that can nullify ninjutsu, creating a real challenge for Naruto and the Enchantress.