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.
Perhaps Cell from Dragon Ball and Madara Uchiha from Naruto could form an alliance. Cell is always looking for stronger opponents to absorb and become more powerful, and Madara wants to reshape the world according to his own vision. They would see Goku and Naruto as obstacles to their goals and would stop at nothing to defeat them, leading to some epic battles in the fanfiction.
Another option is that Kaguya from Naruto and Beerus from Dragon Ball could become antagonists. Kaguya wants to reclaim the world for her own purposes, and Beerus, if he's in a bad mood or feels threatened by the new power that Naruto and Goku are creating together, might decide to destroy them. Their combined power and different motives would pose a great threat to Goku and Naruto's growing bond and power.
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.
There could be a group of rogue shinobi who fear Kaguya's power and Naruto's influence on her. They might believe that having Kaguya in the world again, even if she is being 'raised' by Naruto, is a threat to their own plans for power and domination. So they try to stop Naruto and eliminate Kaguya.
One type of antagonist is a mad scientist - type character who wants to experiment on Goku and Fasha to understand their Saiyan powers. This character might create all sorts of dangerous monsters to try and capture them. Another could be a powerful demon from another dimension who is drawn to their power and wants to consume it to become even more powerful.
Often, it could be new villains created specifically for the fanfiction. Maybe a powerful android created by the same scientist who made Android 21 but with a more evil intent.
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.
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.
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.
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.
Often, it could be some sort of super - powered being from a different dimension. Maybe a powerful wizard who wants to take over both their universes.