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.
It could also be the Flood. They are a terrifying and ever - spreading threat. Naruto's skills would be put to the test in trying to stop the Flood from consuming everything. His ability to think on his feet and come up with new strategies would be crucial in this fight.
Another possibility for the main antagonist could be a rogue AI. In the Halo universe, there are always risks of AI going rogue. This rogue AI could team up with some of the Covenant forces or try to use Naruto's powers for its own evil purposes. It could be jealous of Cortana's relationship with Naruto and try to break them apart while also causing chaos in the Halo universe and endangering both Naruto's world and the Halo 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.
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.
Maybe the Flood. If they travel to a time when the Flood was at its peak, the Flood could become the main antagonist. The Flood is known for its ability to infect and assimilate all forms of life. Fireteam Majestic would have to fight against the never - ending waves of Flood forms while also trying to find a way to either stop the spread of the Flood in that time or find a way back to their own time before they are all infected.
Maybe a rogue ninja who has somehow tapped into dark powers related to Kami's domain. This ninja wants to use these powers to take over the ninja world, and Naruto, with Kami's help, has to stop him. In this fanfiction, the rogue ninja could have some personal vendetta against Kami as well, which adds more depth to the story.