Kabuto could be an antagonist as well. He is a power - hungry character. If Naruto is trying to bring positive change to the Akatsuki, Kabuto's thirst for power and his underhanded tactics could put him in direct conflict with Naruto, as he might see Naruto as a threat to his own plans within the Akatsuki.
One possible plot could be Naruto believing that by joining the Akatsuki, he can change them from the inside. He might think that his influence can stop their more evil plans. For example, he could try to convince them to stop collecting the tailed beasts in a violent way.
It could be an evil wind - based ninja who has been misusing the power of the wind. Naruto gives his body to the wind to combat this antagonist directly on its own element's territory.
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.
Perhaps Kaguya Otsutsuki is resurrected again, but this time with a stronger will and more dangerous plans. Since Naruto was the one who played a major role in defeating her before, she targets him first in this fanfiction.
It could be other villages as well. Since Naruto has made friends and allies from different villages during his adventures. For example, the Sand Village might send some of their ninja to help, considering Naruto's relationship with Gaara.
Sasuke could be a likely candidate. Despite their differences, Sasuke and Naruto have a deep connection. He might hear about Naruto's capture and come to his rescue, driven by their past friendship and the rivalry that also binds them.
The Akatsuki would still likely be the main antagonists. They have their own goals that often conflict with the well - being of the ninja world. Even with Minato alive, they are a powerful and organized group that would pose a great threat.
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 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.
Kakuzu might also be a main antagonist in this fanfiction. He's always after money and power. Maybe he sees Sakura as a valuable asset, either to sell her back to Konoha for a large sum or to use her skills for his own gain. He's not very empathetic and would likely be ruthless in his treatment of her.