Another possibility is that the main antagonist could be the very nature of the dark magic that surrounds Tom. This dark magic could have a will of its own and try to prevent Harry from influencing Tom to take a different path, as it wants Tom to become the dark lord Voldemort.
Maybe it's some dark wizard or a group of dark wizards who don't want Harry to interfere with Tom's development. They see Harry as a threat to their plans of using Tom for their dark purposes in the future.
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.
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 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 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 a new dark wizard who has been secretly building his power. Maybe this wizard uses the allure of the cane and the idea of a new kind of dark magic to draw Harry in. He might be a former follower of Voldemort who has his own plans for domination and sees Harry as a useful tool.
It could be Dumbledore. In a twisted take on the story, if Harry joins the dark side, Dumbledore would be the one trying to stop him. Dumbledore has always been the guiding force for the good side, and Harry's defection would be a huge blow. Dumbledore would then have to face the difficult decision of either trying to save Harry or stopping him by any means necessary, making him the antagonist from Harry's new 'dark' perspective.
Tom Riddle himself could be the main antagonist. Even in his school days, he was showing signs of his future as Voldemort. His dark thoughts and actions towards other students or his exploration of dark magic could put him in direct opposition to Harry.
The main antagonist could be Dumbledore. Since Harry has joined Voldemort, Dumbledore would see Harry as a threat to the good of the wizarding world. Dumbledore would try to bring Harry back to the right side, and they would end up in conflict.
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.
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.