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.
Maybe there could be a new group of villains created specifically for this fanfiction. They could be ninja who oppose Naruto's new Batman - like approach to protecting Konoha. They might see his methods as too radical or a threat to the traditional ninja way, and thus set out to stop him at all costs.
Well, it could be about Naruto being a huge Batman fan in Konoha. Maybe he tries to incorporate Batman's detective skills into his ninja work. He might start wearing a ninja version of the Batman suit and use gadgets inspired by Batman to fight enemies in the Naruto world.
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.
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.
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.
Lex Luthor could be a main antagonist. He might see their union as a threat to his power and schemes, and try to break them apart or use their relationship against them.
The Joker could be a main antagonist. He would be fascinated by Harry's magic and would try to use it for his own evil purposes or just to cause chaos. He might try to drive a wedge between Harry and Batman by using mind games.
Maybe a powerful and corrupted Pokemon that has gained sentience and wants to rule both the Pokemon world and Naruto's world. It sees Naruto as an obstacle because of his godlike powers. This Pokemon could have the ability to control other Pokemon and use them to attack Naruto and those who oppose it. It would be a major antagonist as Naruto has to find a way to defeat it and restore peace to both worlds.