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.
There could be a group of ninja elders in Naruto's world who view the Queen of Demons as a great danger. They don't trust her intentions towards Naruto or the ninja world. So, they become the main antagonists, trying to separate Naruto from the Queen of Demons by any means necessary, even if it means going against Naruto's wishes and putting the whole world at risk.
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.
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.
An ancient evil force that was sealed away by Hashirama long ago could be released in Naruto's time. This entity, having a grudge against Hashirama for imprisoning it, would see Naruto as an obstacle too since he's allied with Hashirama. It could have powers that are completely unknown to the modern ninja world.
It could be Salem herself if the fanfiction focuses on Naruto trying to stop her evil plans. Since Salem has a long history of causing chaos and destruction, Naruto would see her as a force to be reckoned with and try to oppose her.
It could be a rogue ninja from an old clan who has a vendetta against both Konoha and Kumogakure. This ninja has been gathering power in secret and plans to destroy both villages to avenge his clan's past defeat at the hands of the combined forces of the two villages.
It could be a character like Orochimaru who somehow gets access to Gotham's technology and becomes even more powerful. He could be creating new types of jutsu using the advanced tech there and causing chaos in both worlds.
It could be a powerful ninja from Naruto's world who has turned evil and wants to use Lara Croft's knowledge of ancient artifacts for his own gain. He might try to force Lara to lead him to the most powerful artifacts so he can become invincible in both worlds.
Maybe a group of outcast shinobi who are jealous of Naruto's power and Hanabi's connection to the Hyuga clan. They band together to try and take over the village, and Naruto and Hanabi have to stop them. Their leader could be a former Leaf Village ninja who was wronged in the past and now wants revenge.
It could be a character who has the power to absorb chakra and ice magic. Let's call him Zarak. Zarak wants to use the combined power of Naruto's world and Elsa's world to become invincible. He starts by causing chaos in both worlds, making the Hidden Leaf Village believe that Elsa is a threat and making Elsa think that Naruto and his friends are there to capture her. This way, he can keep them apart and continue his evil plan.