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.
Another possibility is that the main antagonist could be a new group or organization that is against both the Akatsuki and the Hidden Leaf. They see Naruto's joining the Akatsuki as a dangerous move that could tip the balance of power in the ninja world. So, they target Naruto and the Akatsuki, making them the protagonists against this new enemy.
Well, perhaps Naruto is heartbroken after losing someone dear, like Sasuke leaving again. He feels betrayed by the Hidden Leaf. In his despair, the Akatsuki approaches him, offering a sense of belonging and a new purpose. They might convince him that the Leaf is corrupt and that their goals, which could be about changing the ninja world in a more radical way, are worth joining.
It could be a new character who has the ability to manipulate people's minds. This character could turn Naruto's friends and the villagers against him by making them believe false things about Naruto. So, this mind - manipulator would be the main antagonist as they are the cause of Naruto's heartbreak.
Perhaps an old enemy of one of the members of Team 9 shows up. Since Naruto has joined the team, they might see it as an opportunity to get revenge. This antagonist could be someone who was once defeated by the member's family and now wants to prove themselves. They would be very cunning and use their knowledge of the team member's past to try and divide the team.
It could be an old enemy who has resurfaced, like Orochimaru again. Since Naruto and Sasuke are together now, Orochimaru might see them as a threat to his own plans for power and immortality.
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.
It could be the leader of the dark guild. This person would likely have a very different ideology from Naruto's. Maybe the leader believes in using extreme and unethical means to gain power, like sacrificing innocent lives for dark magic. Naruto would constantly clash with this leader as he tries to uphold his own values.
Orochimaru could still be the main antagonist. Even if Naruto joins Team Hebi, Orochimaru's motives are often self - serving and evil. He might be using the team for his own experiments or to gain power, and Naruto would oppose that. Naruto's presence in the team could disrupt Orochimaru's plans, leading to a conflict between them.
Orochimaru would likely be a main antagonist even if Naruto joins the Sound Village. Orochimaru has his own devious plans, and Naruto might not fully agree with them. Even though Naruto is in the village, Orochimaru could try to use Naruto for his own gain, like getting access to the Nine - Tails' power. So, Naruto would constantly be at odds with Orochimaru.
It could be a rogue hunter nin who doesn't like the idea of Naruto, an outsider, joining their ranks. This rogue hunter nin might see Naruto as a threat to their power and influence within the group.