It could be a rogue shinobi from Naruto's world who has come to Gotham to steal its technology and use it to create a powerful weapon. This shinobi has the ability to control minds, which makes him a tough opponent for Naruto and Batgirl as he can turn Gotham's citizens against them.
It could be Kaguya Otsutsuki. Since she has powerful abilities and a thirst for power, she would see Kefla's power as a threat and Naruto's influence as something to be eliminated. She might try to manipulate events to turn the ninja world against Kefla and Naruto.
It could be someone who wants to merge their two worlds in a chaotic way. Maybe an evil scientist from Leela's world who has discovered the power of chakra and wants to use it for his own dark purposes. He could try to capture Naruto to study his chakra and use it to take over both universes.
The main antagonist could be an evil merman who wants to take over Ariel's kingdom and is also jealous of her friendship with Naruto. He might use his dark water - based magic to try and stop them.
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 someone who misuses the power of the Hell Girl. Maybe a rogue ninja who discovers the way to summon the Hell Girl and uses her to get rid of his enemies in the ninja world. He doesn't care about the consequences or the morality of it, and Naruto has to stop him from causing more chaos.
Maybe a rogue scientist who has created dangerous mutants and is using them to terrorize the city. This scientist is obsessed with power and sees Hit Girl and Nightbitch as threats to his plans. He would constantly be sending his mutants after them, forcing them to come up with new strategies to fight back.
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.