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.
There could be a group within SHIELD itself that is against having a wizard in their ranks. They might form an underground resistance and become the antagonists, constantly trying to get Harry out of SHIELD while he is trying to do good.
It could be a jealous goblin student who doesn't like an outsider like Harry coming into their academy and stealing the spotlight.
One possibility is that Harry joins SHIELD after realizing the magical world can't fully contain the threats he's faced. In the fanfic, he could be a key figure in bridging the gap between the magical and non - magical worlds within SHIELD. He might introduce magic - based security measures or use his ability to detect dark magic to identify threats that normal technology can't pick up.
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 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.