It could be Voldemort who somehow crosses over into the Naruto world. He would be a formidable antagonist as he has powerful dark magic. He might team up with some of the villains in the Naruto world like Orochimaru, and together they could plot to take over both the wizarding world and the ninja world. Naruto and Harry would then have to work together to stop them.
The Akatsuki could be the main antagonists still. But in this fanfiction, they become more powerful because they learn some magic from Harry's world. They use this new knowledge to enhance their jutsus and become even more of a threat to Naruto. Harry has to figure out a way to counter their new abilities while also protecting Naruto from their attacks. He might also have to deal with some of the Akatsuki members' individual powers which have been amplified by magic.
Perhaps an original character could be the main antagonist. This character could be a powerful ninja who has discovered a way to use dark magic from Harry's world. He wants to use this new power to rule the Naruto world and sees Naruto, with Harry's help, as a threat. So he constantly tries to undermine them and stop their progress. He could also be recruiting other ninjas to his side, creating a large group of enemies for Harry and Naruto to face.
It could be a jealous Slytherin student. Since snakes are often associated with Slytherin, this student might feel that Harry has no right to take care of a snake. They could try to steal the snake or cause trouble for Harry, like spreading rumors that the snake is dangerous and should be removed from Hogwarts.
Maybe it's a dark wizard who has an interest in the snakes Harry is taking care of. He wants to use the snakes for some dark magic purposes. So he constantly tries to steal the snakes from Harry or even harm Harry to get to the snakes. For example, he could be a follower of Voldemort who believes the snakes hold some special power that can help bring back the dark lord.
Iruka and Naruto are the central characters. However, depending on the plot of the fanfiction, characters like the Third Hokage could be involved. He might be the one who gives Iruka certain instructions or permissions regarding Naruto. And then there are Naruto's friends from the academy, such as Kiba and Shino. They could be part of the story, for instance, joining Naruto in some training sessions arranged by Iruka.
Naruto would use his Sharingan - like observational skills. He's used to being aware of his surroundings in the ninja world. So he'd be on high alert for any danger. If any dark wizards came after Harry, Naruto could use his speed to get Harry out of harm's way quickly.
Well, clearly Harry is one of the main characters as he is the one taking care of the baby cousin. The baby cousin is also a main character, even if it's a young and not fully developed character yet.
The main antagonist could be a Slytherin student who has a vendetta against Harry. When they see Harry with the snake, which they believe should belong to a Slytherin, they start causing trouble for Harry. They might try to frame Harry for using dark magic with the snake or try to steal the snake to prove their superiority over Harry.
One possible plot could be that Harry, using his magic skills, protects Naruto from the various threats in the Naruto universe. For example, he could use spells to shield Naruto from enemy ninjas' attacks. He might also use his knowledge of magic to help Naruto understand some concepts that are difficult in the ninja world, like a different way of looking at chakra manipulation which could be related to how magic works in Harry's world.
It could be someone who wants to disrupt the relationship between Naruto and Beerus. Maybe a powerful dark ninja who sees Naruto's newfound connection with Beerus as a threat to his own plans for power.
It could be a rogue ninja from another village who has a vendetta against Konoha. This ninja might target Team 10 specifically because of Naruto's presence, seeing it as an opportunity to make a name for themselves by taking on a powerful shinobi like Naruto.
The Covenant could still be the main antagonists. They are a powerful and menacing force in the Halo universe, and Naruto would have to face their might. Their advanced weaponry and large numbers would pose a great challenge to Naruto.