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 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 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.
It could be a jealous teammate who feels that Harry is getting all the attention and glory. This teammate might try to sabotage Harry during practices or matches.
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.
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.
Dumbledore could be seen as the main antagonist from Harry's new perspective on the dark side. Dumbledore represents all that is good in the wizarding world, and if Harry has turned to the dark, Dumbledore would be the one trying to stop him, to bring him back to the light. So in this context, Dumbledore becomes the opposition that Harry has to face.
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 Thanos. Since he is a powerful and menacing force in Loki's universe. He might see Harry as an unexpected variable and want to eliminate him. Also, his goal of collecting the Infinity Stones could put him at odds with both Harry and Loki as they might try to stop him to protect their respective worlds.
Well, one possibility is that Harry discovers a new sense of purpose and discipline in the military. He might face challenges like tough training, and make new friends who help him grow as a person.