The main antagonist could be an ancient and malevolent entity that has been sealed away for centuries. Naruto and the Spider Queen's new - found alliance and the combined power they are generating could be what accidentally awakens this entity. It then sets out to destroy both of them and everything they hold dear in their respective worlds.
It could be a powerful dark wizard or sorcerer who wants to control both Naruto's world and the Spider Queen's domain. This antagonist might be after the unique powers that Naruto and the Spider Queen possess, like Naruto's chakra and the Spider Queen's web - based magic. He could try to manipulate them against each other to achieve his goals.
It could be a powerful demon who wants to control the Succubus Queen and use her powers for evil. Since Naruto is with the Queen, he becomes a target too.
It could be the other demons who oppose the Queen of Demons' newfound alliance with Naruto. They might see Naruto as a threat to their way of life or as a tool that the Queen of Demons is misusing. So, they would try to break their bond and destroy Naruto.
Maybe a dark ninja clan that has a grudge against Naruto and also wants to control the Vampire Queen for her powers. They would try to set traps for both Naruto and the Queen, making it difficult for them to trust each other and work together against the real threat.
One option could be Kaguya from the Naruto universe. Her god - like powers would pose a great threat to Bayonetta. She could be trying to expand her influence into Bayonetta's world, seeing it as a new place to conquer.
It could be a dark wizard who wants to capture the nymph for her powers. He sees the nymph's connection to nature and wants to use it to gain ultimate power in the Naruto world.
It could be a rogue ninja who has also discovered a way to harness the power of Amaterasu in a corrupt way. This ninja might want to use the power to take over the ninja villages and Naruto stands in his way.
It could be an evil ninja from Naruto's world who has somehow gained the ability to control Digimon. He wants to use this power to rule over both worlds. He targets Renamon because of her connection to Naruto and tries to break their bond. He might also be after the special powers that Naruto and Renamon possess when they work together.
It could be a rogue ninja who has a vendetta against Naruto and sees Heather as a way to get to him. Maybe this ninja was once defeated by Naruto and now wants to use Heather as bait or hurt her to break Naruto's spirit.
Perhaps a rogue ninja who has learned about the mummy's existence and wants to sell it to the highest bidder. He will stop at nothing to get the mummy, even if it means fighting Naruto and causing chaos in the process.
The Akatsuki could also serve as the main antagonists. They might view Naruto and Midnight as threats to their plans. For instance, if they find out that Midnight has some knowledge or power that could disrupt their collection of tailed beasts, they would target them. Naruto and Midnight would then have to fight against the Akatsuki's various members, each with their own dangerous abilities.