Maybe some new villains from the multiverse. As Loki and Peter start exploring different realms together, they could encounter beings who want to use Peter's powers for their own evil plans. These villains might be powerful magic - users or creatures that are not from Earth and have different motives and abilities.
Maybe some dark elves or other villains from the Marvel universe. They could see the baby as a valuable asset or a threat, and try to harm the baby or use it against Loki. Since Loki is now responsible for the baby, he has to fend off these threats to keep the baby safe. For instance, the dark elves might think the baby has some special power and they want to harness it for their own evil purposes.
One possible antagonist could be Sabretooth. He might see Wolverine's newfound fatherly relationship with Peter as a weakness and try to use Peter to get to Wolverine. Sabretooth could be jealous of the bond Wolverine is forming and want to destroy it.
Perhaps in this fanfiction, Loki adopts Peter because he sees potential in him. Peter, being young and inexperienced in some aspects of the wider universe, can be molded by Loki. Loki could use his cunning and knowledge to train Peter not just in combat but also in the art of deception, which could be useful for Peter in his superhero life. They might start by Loki stealing Peter away from his normal life for a short time to show him a different side of existence.
Loki is known for his mischievous nature. In this fanfiction, he could bring out a more playful side in Peter. Peter might start to use his powers in more creative and unexpected ways, like using his web - slinging not just for fighting and swinging around, but also for creating elaborate pranks, inspired by Loki. Also, Loki's manipulative side could either make Peter more distrustful of others or teach him how to spot manipulation better, depending on how their relationship develops.
In a 'Loki adopts Peter Parker' fanfiction, Loki might teach Peter some of his trickster ways. Maybe he'd show Peter how to deceive enemies in a more magical way than just using his Spidey - sense. For example, Loki could teach Peter how to create illusions to confuse villains during a fight.
In the Naruto world, it could be Orochimaru. He might be interested in Naruto's newfound Pokémon - related powers and try to capture him to experiment on him. Orochimaru is always after power, and Naruto's unique abilities could be very appealing to him.
One possible main antagonist could be Frieza. Imagine if Frieza somehow found his way into the Naruto universe. He would be attracted to the chaos and power struggles there. Goku and Naruto would have to team up to stop him from taking over the Naruto world. Frieza's cold - blooded nature and his desire for power would put him at odds with our heroes. His powerful abilities would be a huge threat to both Naruto and Goku, especially since Naruto is still learning about the new powers Goku is teaching him.
Another possibility is that some rogue ninja who have a vendetta against Hanzo might target Naruto as a way to get back at Hanzo. They could see Naruto as Hanzo's weakness and try to harm or kidnap him, which would then lead to a series of battles and confrontations in the fanfiction.
The main antagonists could be the traditional enemies of Camelot like Morgana. She might see Merlin's act of adopting Mordred as a threat to her plans. Also, some of the knights or nobles in Camelot who are superstitious and believe Mordred is a danger just because of the prophecies could be antagonists. They might try to separate Merlin and Mordred or even harm Mordred.
Obviously, Pepper and Peter are the main characters. Pepper, with her strong and capable personality, and Peter, the young and enthusiastic Spider - Man.