Perhaps the main antagonists would be the dark forces in the universe that are threatened by the growing power of the Loki - Naruto duo. These could be powerful sorcerers or ancient evils. Or, it could be Loki's own family members who oppose his newfound relationship with Naruto, seeing it as a distraction from his duties in Asgard.
In this 'naruto adopted by loki fanfiction', the main antagonists might be a group of interdimensional beings. They notice the unique combination of Naruto's ninja powers and Loki's magic and see it as a threat to their plans of universal domination. Additionally, there could be some jealous Asgardian warriors who feel that Loki is giving Naruto too much attention and they try to undermine their relationship.
It could be that Kaguya Otsutsuki resurfaces in this fanfiction. Since Naruto is now under Sesshomaru's wing and growing in power, she sees him as a threat to her plans of ruling over all worlds. And from Sesshomaru's side of the story, there might be a powerful demon lord who doesn't like Sesshomaru taking in a human - like Naruto and decides to oppose them both.
Another possibility is that some of the more power - hungry ninja from Naruto's own world might become antagonists. They could be jealous of Naruto's new connection with Ryu Hayabusa and the potential power and knowledge he could gain from it. These ninja might try to undermine Naruto or even try to harm Ryu to prevent Naruto from getting stronger. Maybe some of the rogue ninja or the hidden enemies within the ninja villages would see this as an opportunity to make a move against Naruto.
The shinobi council could be antagonists. They would be very suspicious of Naruto being adopted by Jenova, fearing that he will bring destruction to the village. They might try to isolate or even eliminate Naruto.
Well, it could be really wild. Naruto's energetic and determined nature might clash or blend well with Loki's mischievousness. Maybe Loki sees something in Naruto that reminds him of himself, like being an outcast in a way. He could teach Naruto some of his magic tricks, and Naruto could show Loki the value of true friendship and loyalty.
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.
It could be some of the more powerful villains from both universes combined. Maybe Frieza and Orochimaru team up. Frieza's lust for power and Orochimaru's desire for immortality and knowledge would make them a formidable pair. They would target Naruto because of his potential and Goku because of his strength, aiming to either destroy them or use them for their own evil purposes.
The main antagonists in a naruto modern time fanfiction could be a cult - like group that believes in an ancient and dark ninja ideology. They might try to disrupt modern society by using forbidden ninja techniques. Or it could be a political faction that wants to control the ninja population for their own gain. There's also the possibility of a cyber - terrorist group that targets ninja - related facilities using modern technology against the traditional ninja ways.
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.
It could be a group of powerful warlords or samurai who oppose Naruto's new - fangled ideas. They might see his ninja - like abilities as a threat to the traditional order of the Taisho period.
It could be Orochimaru. Since Naruto is taking on a more Batman - like role, Orochimaru's sneaky and often - hidden nature would make him a great antagonist. He would be like the Joker to Naruto's Batman, constantly causing chaos and trying to undermine Naruto's attempts to protect Konoha.