There might be some ancient forces or entities that are awakened by Naruto and Sasuke's new 'godlike' status. These could be demons or spirits that were sealed long ago and now see Naruto and Sasuke as threats to their plans of domination. They would be very powerful and require Naruto and Sasuke to use all of their enhanced abilities to defeat.
It could be a rogue ninja who is jealous of Naruto's godlike powers and wants to take them for himself. This ninja might target Naruko as a way to get to Naruto.
It could be the other Hidden Villages. Since Naruto is becoming so powerful under Danzo's training, they might see him as a threat and try to stop him. Maybe they would send their best ninjas to take him down.
Maybe there's a rogue ninja who has developed a new and dangerous jutsu that can counter Naruto's powers. This ninja wants to prove himself as the strongest by defeating Naruto and taking over the bijuu's power. He might be jealous of Naruto's newfound status and the respect he gets from the other ninjas.
It could be a group of rogue ninjas who want to steal Naruto's godlike powers for themselves. They might be led by a powerful and evil ninja who has his own motives for wanting such power.
Maybe an ancient evil that has been awakened. This entity is so powerful that it takes the combined godlike powers of Naruto and Kushina to stand against it. The antagonist could have some connection to the origin of chakra or an old, forgotten curse.
The main antagonists could also be a group of rogue ninjas who have made a pact with some meta - humans from the Flash's world. They could be after Naruto because they want to use his connection to Barry Allen to gain access to the Speed Force. These antagonists would be a combination of the stealth and trickery of ninjas and the super - powers of meta - humans. They could create a lot of chaos in both the Naruto and Flash worlds, forcing Naruto to use all of his newly acquired skills and powers to stop them.
There could be an outside force, like a neighboring village that wants to keep Naruto and Sasuke away from their own village. They might be afraid of the potential power and influence Naruto and Sasuke could bring back if they return. So, this neighboring village sends their best ninjas to hunt down Naruto and Sasuke during their banishment, making them the main antagonists in the fanfiction.
Perhaps there are dark forces from another dimension. These forces might be attracted to Naruto's power and want to either steal it or destroy him to prevent him from using it against them. They could be powerful demons or sorcerers with their own motives.
Another possibility is that the main antagonists could be the leaders of the other ninja villages. They might view Naruto's godlike and rogue status as a danger to the balance of power among the villages. So, they could form an alliance against Naruto, leading to a lot of political intrigue and conflict in the story.
There could be a mysterious organization that has been hidden for a long time. They emerge when Sasuke and Sakura start their journey. This organization wants to use Sasuke's power and Sakura's medical knowledge for their own evil purposes. They set up traps and send assassins to target the duo throughout their journey.