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.
Another option is an otherworldly demon that has entered their dimension. It has powers that are beyond what they've ever faced before. The demon is bent on destruction and chaos, and it takes all of Hit Girl's combat skills and Nightbitch's special powers to even stand a chance against it.
One idea could be that they team up to fight a common enemy in a world where the bad guys are more powerful than ever. They combine their unique skills, Hit Girl's martial arts and Nightbitch's special abilities, to take on this new threat.
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.
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 another powerful villain from the Dragon Ball universe like Cell. Since Gohan and Frieza are starting to form an unlikely bond, Cell might see this as a threat to his own plans of domination. He could try to break them apart and defeat them both.
The Green Goblin could be a great antagonist. He might see the two spiders as a threat to his plans of taking over the city and decides to target them both. His maniacal nature and his array of dangerous gadgets would pose a serious challenge to Spiderman and Spider Girl.
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.
It could be a group of Quincy who have decided that Ichigo and Yoruichi are a threat to their new order. They believe that Ichigo's hybrid nature and Yoruichi's knowledge and power are things that could disrupt their plans to reshape the spiritual world. So, they start a campaign to eliminate them. This group of Quincy is led by a fanatical leader who is willing to do whatever it takes to achieve their goals, even if it means using dark and forbidden Quincy techniques.
It could be a new, powerful blader who wants to take over the beyblade world. He sees Dynamis and Rago as threats and tries to eliminate them one by one.