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.
Beerus would likely be more powerful. He is a god of destruction in his own universe with incredible cosmic powers. Naruto is extremely powerful in his world, but his power is mostly based on chakra and ninjutsu, which is on a much smaller scale compared to Beerus' ability to destroy planets with a flick of his finger.
A powerful, ancient being from a forgotten universe could be the main antagonist. This being could be jealous of Beerus and Champa's power and status, and decides to challenge them to take over their universes.
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.
Another possibility is that the wizarding world in the Harry Potter side of the fanfiction might see Naruto as a new threat similar to Voldemort. So, some powerful wizards could come to the Naruto world to stop Naruto from becoming too much like Voldemort, thus making them the antagonists in this strange crossover fanfiction.
It could be a character who wants to steal Brook's musical powers. Maybe a dark wizard from a third world who has heard of Brook's ability to control people's emotions with his music. He sees Naruto as an obstacle in his way to getting to Brook.
It could be a rogue sea god who is jealous of Poseidon's power and wants to use Naruto to get to him. This sea god might try to manipulate Naruto into believing that Poseidon is a threat to his village and convince him to attack Poseidon first.
It could be a rogue ninja who has always been envious of Naruto's popularity and power. He sees the Purge as the perfect chance to get rid of Naruto once and for all and take over the Hidden Leaf Village. He might form a group of like - minded ninjas who are also tired of living under the rules and want to create their own chaos during the Purge.
Another option could be an evil wizard in the Cinderella world who sees Naruto as a threat to his control. He might try to keep Cinderella in her oppressed state to prevent her from getting closer to Naruto, who has the potential to bring new ideas and power that could undermine the wizard's authority.
It could be Frieza. Frieza might sense Gohan getting stronger under Beerus' training and see him as a threat. He decides to stop Gohan's progress by any means necessary.