It could be a jealous goblin student who doesn't like an outsider like Harry coming into their academy and stealing the spotlight.
Well, perhaps in this fanfic, the Goblin Academy has some sort of problem that only Harry can solve. He joins to help them out, and along the way, he makes new friends among the goblin students. He might also learn about goblin history and magic that is different from what he knows at Hogwarts.
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 headmaster of the imperial academy. They would be in charge of making sure all the students adhere to the Empire's values and teachings. They might see Luke as a potential threat to their regime within the academy and constantly try to undermine him or turn him into a loyal imperial subject.
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.
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 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.
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.
It could be some of the pure - blood wizard families who have always looked down on goblins and consider them as inferior beings. They might oppose Harry's attempts to defend the goblin because it goes against their traditional views of the wizard - goblin hierarchy.