Perhaps a new character, a dark sorcerer who wants to merge the two worlds into a chaotic realm where he can rule. He sees Naruto's chakra and Gwen's powers as the keys to unlocking this new world. He'd start by pitting Naruto and Gwen against each other, creating misunderstandings, before revealing his true plan and forcing them to team up to stop him.
It could be Orochimaru. He's always interested in new forms of power. When he hears about Gwen Stacy's unique abilities from another world, he'd be eager to capture her and study her. He might think her spider - like powers could be used to enhance his own jutsu or even find a way to gain immortality in a different way.
It could be the Green Goblin. He might see the baby as a way to get back at Peter. Maybe he thinks that by kidnapping the baby, he can force Peter to make some sort of deal or just to cause him great pain.
Peter Parker is one of the main characters. He has a deep connection with Gwen. Her father is also important. He's often concerned about Gwen's safety in the dangerous world of the comic. And there are the villains like the Green Goblin who play a major role in the story.
Gwen Stacy was an important figure in the Spider-Man comic universe. She was smart, kind, and had a complex relationship with Peter Parker. Her death had a huge impact on the story.
One possible plot could be that Gwen Stacy somehow gets transported to the Naruto universe. She could meet Naruto and his friends, and they initially mistake her for a strange ninja from a far - off land. Gwen, with her scientific knowledge and acrobatic skills, could try to find a way back home while also helping the ninja in their battles against enemies. For example, she might use her knowledge of physics to create new jutsu - like techniques.
The Green Goblin killed Gwen Stacy in the comics. It was a tragic moment that had a significant impact on the storyline.
It could be someone who wants to disrupt the relationship between Naruto and Beerus. Maybe a powerful dark ninja who sees Naruto's newfound connection with Beerus as a threat to his own plans for power.
It could be a rogue ninja from another village who has a vendetta against Konoha. This ninja might target Team 10 specifically because of Naruto's presence, seeing it as an opportunity to make a name for themselves by taking on a powerful shinobi like Naruto.
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.
Another possibility is that the wizarding world in the Harry Potter side of the fanfiction might see Naruto as a new threat similar to Voldemort. So, some powerful wizards could come to the Naruto world to stop Naruto from becoming too much like Voldemort, thus making them the antagonists in this strange crossover fanfiction.
It could be a character who wants to steal Brook's musical powers. Maybe a dark wizard from a third world who has heard of Brook's ability to control people's emotions with his music. He sees Naruto as an obstacle in his way to getting to Brook.