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.
A Naruto x Cortana Halo crossover fanfiction could involve Naruto being mistaken for a new type of Spartan. Cortana would be intrigued by his unique abilities. She could try to analyze his chakra flow as if it was some new form of energy in the Halo world. Naruto, on the other hand, would be in awe of the advanced technology and might learn to use some Halo weapons in his own ninja - style way.
The Covenant could still be the main antagonists. They are a powerful and menacing force in the Halo universe, and Naruto would have to face their might. Their advanced weaponry and large numbers would pose a great challenge to Naruto.
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.
Their interaction would be really unique. Naruto is all about physical combat and using chakra, while Cortana is a digital intelligence. Naruto might see Cortana as a new kind of ally, someone he can trust. He would probably be curious about her abilities and try to learn from her. Cortana, on the other hand, would be intrigued by Naruto's powers and his unwavering determination.
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 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.
It could be an old enemy of Kushina's who was thought to be dead but has now returned. Maybe someone from her days in the Uzumaki clan who has a vendetta against her and now sees Naruto as an obstacle too.
The main antagonist could be a combined form of Kaguya from Naruto and Elizabeth Greene from Prototype. Kaguya's god - like powers combined with Greene's virus - based abilities would make for a truly terrifying foe. She could be trying to merge the two worlds into one chaotic mess where she can rule supreme, using the shinobi's chakra and the virus - infected creatures to her advantage.