It could be Orochimaru. He might be interested in Ino's mind - control abilities and Naruto's Nine - Tails chakra for his own evil experiments. He could try to capture them both and use their powers to create a new type of jutsu or even a new, more powerful being under his control.
Madara Uchiha could still be a great antagonist. Even with Itachi and Naruto teaming up, Madara's power and his long - term plans for the ninja world would pose a huge threat. His knowledge of the Sharingan and his connection to the Uchiha clan would make for an interesting conflict against Itachi, while his overall strength would be a challenge for Naruto as well.
It could be someone like Doctor Octopus who gets his hands on some ninja technology. He could use it to enhance his mechanical arms and also start stealing chakra from people to power his new devices. His scientific mind combined with the newfound ninja powers would make him a formidable foe for Naruto and Spiderman.
It could be Orochimaru. He's always had his eyes on Sasuke and Naruto has also been in his crosshairs. He could return with some new and more powerful jutsu, forcing Naruto and Sasuke to put aside their differences and fight him together. Maybe he has a plan to take over the entire ninja world this time.
It could be Orochimaru. He's always interested in new powers and artifacts. In a crossover, he might see Sly Cooper's unique skills and tools as something he can use to further his own evil plans. He could also try to use Sly to steal secrets from other ninja villages. And of course, he would be a big threat to Naruto as well.
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.
Another possibility for the main antagonist could be a rogue AI. In the Halo universe, there are always risks of AI going rogue. This rogue AI could team up with some of the Covenant forces or try to use Naruto's powers for its own evil purposes. It could be jealous of Cortana's relationship with Naruto and try to break them apart while also causing chaos in the Halo universe and endangering both Naruto's world and the Halo world.
It could be Sasuke. He has had his own dark journey and might turn against Naruto and Ino in this fanfiction. His newfound power and different ideals could make him see Naruto and Ino as threats to his goals.
It could be an unknown enemy who is manipulating Dark Naruto's use of Ino's kunai. This enemy might have a vendetta against the Hidden Leaf and sees Dark Naruto as a tool. They secretly guide him in misusing the kunai to achieve their own evil goals.
Perhaps an ancient evil that has been sealed away in the empire for centuries but is released due to the chaos of the crossover. This entity could be more powerful than any foe the Naruto characters have faced before, forcing them to find new ways to fight.
A group of rogue shinobi and some of Daria's school bullies could team up. The shinobi would give the bullies some ninja powers, and together they would cause trouble in both worlds. This group would be difficult to deal with as they combine the physical strength of the shinobi with the local knowledge of the bullies.