In this kind of fanfiction, the main antagonist could be a new character created out of the chaos caused by the merge. For example, the merge could disrupt the balance of the ninja world in a way that awakens an ancient evil force that was sealed away long ago. This force would see the merged Naruto - Madara as a target to destroy because they represent a new power that could oppose it.
Well, in this 'naruto in madara merge fanfiction', Naruto's will of fire could be merged with Madara's long - held beliefs. This could lead to a whole new way of looking at the ninja world. They might use their combined power to reshape the shinobi society, for better or for worse. For example, they could end all the wars in the ninja world by imposing a new set of rules that are based on their combined ideology.
Maybe an old enemy of Madara who realizes that by targeting Naruto, he can get back at Madara. Since Madara has some sort of connection or interest in saving Naruto in this fanfiction, the enemy thinks that if he can harm Naruto, he can either draw Madara out or simply cause him pain. This enemy could be a powerful rogue ninja with a vendetta against Madara.
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 another powerful ninja who sees the student as a threat to their own power or plans. Maybe someone who doesn't want Madara to pass on his knowledge to an outsider or a young upstart.
It could be Orochimaru. He might see Nicki Minaj's unique abilities as a threat to his plans of world domination. He could try to kidnap her to study her powers and use them for his own evil purposes. Naruto would then have to rescue her and stop Orochimaru once again.