Maybe a new character that combines the worst traits of both universes. For example, a ninja - like thief who has the ability to use some form of dark chakra and also has Sly Cooper's stealth skills but uses them for evil. This character could be after a powerful object that has significance in both the Naruto world and Sly's world, and Naruto and Sly have to stop him.
Danzo could be a great antagonist. He's always been a shadowy figure in the Naruto world, willing to do whatever it takes to achieve his goals. In a crossover, he might see Sly Cooper as a threat to his control. He could try to capture Sly and use his skills for his own purposes. He would also be against Naruto if Naruto teams up with Sly, as Danzo doesn't like things that are out of his control.
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.
The main characters would be Sly Cooper and a Pokemon like Eevee. Eevee has the ability to evolve into different forms, which could add an interesting element to the story. Sly Cooper could befriend Eevee and together they face various challenges. There might also be some secondary characters like Sly Cooper's gang members and other Pokemon trainers or Pokemon that they encounter during their adventures in the crossover world.
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.
One possible plot could be that Sly Cooper is on a heist in a world that has some sort of connection to the Naruto universe. Maybe he's stealing a valuable scroll that contains a powerful jutsu. Naruto, being the curious and justice - loving ninja he is, mistakes Sly for a bad guy at first. But as they interact, they realize they can help each other. Sly can use his thieving skills to get some intel for Naruto about an enemy ninja group, and Naruto can protect Sly from the more dangerous ninja threats.
Ratchet would probably be a bit suspicious of Sly at first. He's used to dealing with more straightforward enemies. But Sly's charm might win him over. Sly, on the other hand, would be intrigued by Ratchet's high - tech gadgets and might try to steal one or two just for fun.
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.
Sly would probably be initially shocked. But then he'd be overjoyed. He'd start making plans to keep her and the baby safe. He might even consider retiring from his thieving ways to be a full - time family man.
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.