The power balance would be completely disrupted. Without the ninja villages, there would be no organized ninja forces. This could lead to smaller groups or individuals vying for power, causing chaos everywhere.
It could be a result of a prophecy misinterpreted. He might believe that destroying the ninja villages is the key to fulfilling some grand prophecy that he thinks will ultimately lead to peace, not realizing the true meaning of the prophecy which has been distorted by false information.
It could be a fan - made concept where in a fanfiction Naruto somehow has a scenario where he destroys things related to Fairy Tail. Maybe it's a crossover idea where Naruto's powers are pitted against the world of Fairy Tail and he causes destruction within that fictional setting.
Perhaps Naruto uses his newfound mastery of all ninja arts to defend the ninja world from a powerful and previously unbeatable enemy. He could combine different arts in creative ways to outwit the foe. For example, using water jutsu in combination with earth jutsu to create a new kind of defensive or offensive move.
It could be Sasuke. If he were to turn to the dark side in the fanfiction, his Rinnegan powers could be used to destroy Konoha. He has the potential to be extremely powerful and if he has some sort of vendetta or is influenced by some dark force, he might take his anger out on the village.
One interesting masked ninja is Shinji. He is a masked character in fanfiction who was once a normal ninja but got cursed by an ancient evil. Now, with his masked identity, he tries to find a way to break the curse while also using his new - found dark powers for good in the Naruto world. There's also a masked ninja named Yuki. Yuki is a snow - style user and her mask is made of ice crystals. She is on a quest to find the origin of her ice - based powers. Another is Hikaru, a masked ninja with the power of light, who is often at odds with the darker elements in the Naruto fanfiction world.
It could be a group of rogue ninja who are jealous of Naruto's new powers. They might band together to try and steal his knowledge of all ninja arts or defeat him to prove their own superiority.
Madara Uchiha could also be a possible antagonist in this scenario. Even if he is dead in the original story, in a fanfiction, his lingering influence or a resurrected form could manipulate Naruto. Madara was always against Konoha's ideals to some extent and might use Naruto as a tool to destroy what he hated.