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.
Another possibility is a new, unknown force. Maybe there is an ancient evil that has been awakened by the combined power of Naruto and Obito. This entity could see their alliance as a means to gain more power in the ninja world and tries to destroy them before they can fully realize their potential. It could be a powerful demon or a group of rogue ninjas with dark intentions.
In a 'naruto joins obito fanfic', it could start with Naruto being transported to a parallel dimension where Obito has already started his own ninja village. Naruto, seeing the potential in Obito's ideas but also the flaws, decides to join him. He helps Obito to correct his path. For example, Naruto could teach the ninjas in Obito's village about the importance of hope and not giving in to hatred. They could then work together to build a village that is a model for the rest of the ninja world, based on both Obito's and Naruto's ideals.
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.
Maybe a new character created specifically for this fanfic. A powerful sorcerer who wants to use Naruto's chakra and Slade's combat expertise for his own evil purposes. He could be manipulating events from the shadows, pitting Naruto and Slade against each other at first until they realize they are being played.
It could be an old enemy of the Hunters. Maybe a powerful monster that has a grudge against them for past defeats. For instance, a giant who has been waiting for the right time to strike back at the Hunters.
It could be a rogue wizard who has infiltrated SHIELD and is using their technology for dark magic purposes. This wizard might be jealous of Harry's new position and try to undermine him.
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.