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.
Well, one type of antagonist could be a group of ninjas who were once shunned by society and now seek revenge in the modern world. They might have new and dangerous abilities. Another could be a powerful figure in the business world who wants to monopolize the use of ninja powers for profit. And then there could be a shadowy organization that secretly hunts down and captures ninjas for their own unknown and sinister purposes in this modern setting.
It could be a group of corrupt business people. They use their wealth and influence to manipulate the city's economy and politics for their own gain. Naruto, with his sense of justice, would oppose them. For instance, they might be trying to close down a community center that helps underprivileged kids, and Naruto steps in to stop them.
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.
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.
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.
It really depends on the specific fanfiction. However, it could be that they travel back to a time when Orochimaru was at his most devious, so he would be a main antagonist. His experiments and thirst for power could pose a great threat to Naruto and Shikamaru's mission in the past.
Often, it could be the same antagonists from the original Naruto series but in a different context. For example, Orochimaru might still be an antagonist if he tries to use the time - travel situation to his advantage, like getting his hands on some ancient forbidden jutsu.
It could be some of the historical villains from Naruto's past that were thought to be long gone but are now resurfacing due to the time travel. For example, Madara Uchiha might be an antagonist if they travel back to a time when he was still active and plotting against Konoha.