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.
Madara could also save Naruto by using his knowledge of the ninja world. Maybe he has some inside information about a plot against Naruto and he intervenes in time to stop it. He might have discovered a secret plan by an enemy group and takes action to keep Naruto out of harm's way. This could involve manipulating events behind the scenes or directly confronting the threat.
One possible plot could be that Madara, seeing Naruto in a dangerous situation related to a love interest, decides to step in. Maybe Naruto's love is being threatened by an enemy who wants to use their relationship for some dark purpose. Madara, with his powerful abilities, fends off the enemy and in the process, Naruto realizes Madara has a more complex side than he thought. This could lead to a change in their relationship dynamic, perhaps even a friendship that forms the basis for some interesting interactions in the future of the fanfiction.
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.
It could be a rogue ninja from Tobirama's time who has a vendetta against the Senju clan. This ninja might have been waiting for the perfect moment to strike at Tobirama when he is alone or vulnerable. Naruto then has to face this powerful and vengeful enemy to save Tobirama.
It could be a rogue ninja who is using the poochyena for some sort of evil experiment. Naruto has to stop this ninja from harming the poochyena.
It could be someone like Madara Uchiha. He's extremely powerful and his goals are often in conflict with Naruto's. Goku would have to face his Sharingan abilities and his vast array of jutsu.
Perhaps a new and original antagonist could be created for this fanfiction. This antagonist could be a rogue ninja who has mastered a forbidden jutsu that allows him to manipulate time as well. He could be the one who sets up the events that lead to Minato's endangerment, and Naruto has to figure out his motives and stop him while also saving Minato.
Perhaps it's a group of mercenary ninjas. They've been hired by someone who has a grudge against Zabuza. They see Zabuza as an easy target when he's alone or vulnerable, but Naruto shows up to spoil their plan.
Maybe it's an ancient evil entity that has been awakened by the combined power of Naruto's chakra and Wonder Woman's divine energy. This entity sees them as a threat to its plan of ruling both universes and thus tries to eliminate Wonder Woman first, which is when Naruto steps in to save her.
One possible plot development could be that after saving Naruto, Madara tries to mentor him. He sees Naruto's potential and wants to shape him into an even greater ninja, sharing his own knowledge and skills that have been honed over years.