Perhaps the main antagonist is an ancient evil that has been awakened. This evil force realizes that Naruto and Team 7 together could be a threat to its plans. So it uses its dark powers to influence the minds of the village leaders, making them order Team 7 to abandon Naruto. As Naruto struggles alone, the evil force tries to stop him from reuniting with his team and growing stronger.
Another possible main antagonist could be a rogue ninja from a different village. This ninja could be jealous of Naruto's growing power and popularity. So he devises a plan to frame Naruto, making it seem like he's a danger to the village. This causes Team 7 to be pressured into abandoning him. The rogue ninja then continues to cause trouble for Naruto as he tries to clear his name.
It could be Danzo. He's always been a bit of a shadowy figure in the Naruto series. Maybe he sees Naruto as a threat to his power and influence in the village and manipulates the situation so that Team 7 has to abandon him. He would be a great main antagonist as he has the resources and the motives to cause such a rift in Team 7.
Perhaps the main antagonist is actually an old enemy who manipulates Naruto's team into abandoning him. This enemy could be using mind - control or false information to drive a wedge between Naruto and his team. They do this to weaken Naruto, knowing that his strength comes from his relationships.
It could be a rogue ninja from a rival village. This ninja has a personal vendetta against Konoha and specifically targets Team 10 because of Naruto's presence. He might be jealous of Naruto's growing power and fame and wants to prove himself by defeating the team.
Another possibility is a power - hungry ninja within the village who wants to take advantage of Sakura's situation. They might try to manipulate her or use her as a pawn in their scheme to gain more power. Since she's been abandoned, she may be more desperate and easier to influence, making her a prime target for this type of antagonist.
It could be the elders of his clan. They are often the ones who make decisions in the clan, and if they see Naruto as a threat for whatever reason, they could be the main antagonists. They might be afraid of Naruto's growing power or his different way of thinking that could disrupt the traditional ways of the clan.
Maybe the main antagonist is the entire Iwa council. They might be the ones who order Naruto's abandonment because they fear his potential influence on Iwa. They would do everything in their power to keep him from uncovering their plans or causing unrest among the villagers.
The Akatsuki could be the main antagonist. They might see Hanzo as an easy target after Naruto abandons him and try to capture him for their own purposes, like using his knowledge of the ninja world or his unique abilities.
It could be someone from the village who doesn't want Naruto to discover the truth about his parents. Maybe they fear that if Naruto finds out certain secrets, it will disrupt the power balance in the village.
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 a relative from his family who was behind the abandonment. Maybe they want to keep Naruto away from some family secret or power, and they will do anything to stop him from finding out the truth.
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.