It could be a particular Black Ajah sister who has her own agenda. She might be the one who convinces Rand to join willingly. She could be using her charm or false prophecies to make Rand believe that he is doing the right thing, all while she is the real force working against him and the world's good.
Most likely, the leaders of the Black Ajah would be the main antagonists. They would be manipulating Rand for their own ends, perhaps to use his power for some dark ritual or to further their control over the world of the Wheel of Time.
Maybe Rand is deceived by false promises of power within the Black Ajah. He might think that by joining them, he can gain more control over the One Power or have a better chance at achieving his goals. However, he soon realizes the true evil nature of the Black Ajah.
It could be a senior officer who has a grudge against Percy for some reason. Maybe Percy accidentally made him look bad in front of the higher - ups early on.
There might be a supernatural or magical antagonist, even in a military setting. This could be a dark wizard or a creature that has infiltrated the military for its own malicious purposes. Harry, with his experience in the magical world, would be the key to dealing with this threat, but he has to convince the non - magical military personnel of the danger first.
It could be one of the traditional Volturi members who oppose Edward's presence. They might see him as an outsider who could disrupt their long - established order. For example, Caius might be against Edward joining as he's often portrayed as more rigid and less accepting of new vampires in the Volturi.
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 Voldemort. Imagine if he somehow found a way to cross over into the world of the Fellowship. He would be a powerful and menacing antagonist, using his dark magic to oppose both Harry and the Fellowship.
It could be Voldemort. Even if it's a fanfiction where Harry joins Tom, Voldemort's future self might still be a threat and oppose Harry's attempts to change Tom.
It might be an alien race that has the ability to travel through the earth's crust undetected. They are stealing valuable resources from the planet's core. The Avengers, including Quake, are the only ones who can stop them. The aliens' technology and physical abilities make them a formidable foe, and Quake has to use her powers in creative ways to expose and fight 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 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.