Maybe an external force could be the main antagonist. For instance, a new group that has a vendetta against both the Akatsuki and Miyu. They might see the Akatsuki's interest in Miyu as a threat to their own plans, so they try to stop both. This would force the Akatsuki and Miyu into an uneasy alliance against this new common enemy.
It's also possible that Miyu herself could be seen as the main antagonist from the Akatsuki's perspective. If her power is too uncontrollable or if she refuses to cooperate with them in any way, they might view her as a problem that needs to be eliminated. So in this case, the Akatsuki would be constantly trying to either subdue or get rid of Miyu.
Well, it could be about Miyu being a new character who gets involved with the Akatsuki. Maybe she has some special power that they want to use for their own goals. For example, she could have the ability to find rare chakra sources, and the Akatsuki tries to persuade her to join them.
One common theme is loyalty. Miyu often has to decide where her loyalties lie, whether it's with the Akatsuki or with other characters she meets in the Naruto world.
It could be the Hidden Leaf Village itself. Since Naruto was neglected there, the village's leadership or some of the villagers who shunned him could be seen as antagonists. They pushed Naruto towards the Akatsuki by not giving him the support he needed.
Maybe Danzō could be the main antagonist. Even before Naruto joins the Akatsuki, Danzō has always been a shadowy figure with his own agenda in the Leaf. If Naruto is heartbroken because of Danzō's actions, like ordering the death of someone Naruto cares about, and then joins the Akatsuki, Danzō would still be the one trying to undermine Naruto and the Akatsuki's new - found alliance.
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 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.
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.