In 'naruto joins team 9 fanfiction', the main antagonist could be a powerful group from another village. They see Naruto joining Team 9 as a sign that the Hidden Leaf is getting stronger. So, they send their best warriors to take on Team 9 and try to stop Naruto from growing. This group might have some dark and forbidden jutsu that they are not afraid to use against the team.
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.
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.
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 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.
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 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.
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.
The main antagonist could be Madara. Even though Obito was once following Madara's plan, with Naruto joining Obito, Madara might see this as a threat to his grand scheme. He could try to manipulate events to drive a wedge between Naruto and Obito or directly attack them to stop their new alliance from achieving their goals.
Maybe there's a corrupt elder in Iwa who doesn't trust outsiders. This elder sees Naruto as a threat to Iwa's traditional ways and tries to get rid of him. He might spread false rumors about Naruto within the village and try to turn the other ninjas against him.
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.