There's also the possibility that a group of rogue ninjas, who have banded together after being ostracized for their interest in the godlike hollow powers, become the antagonists. They might believe that Naruto is misusing or hoarding these powers and decide to take them by force, leading to a series of intense battles between them and Naruto.
It could be a powerful ninja who has been corrupted by Hollow powers. He or she might have sought out these powers in a quest for ultimate strength and then turned on the Hidden Villages. This character would use their new - found Hollow - like abilities, such as high - speed regeneration and powerful energy attacks, to cause chaos.
Another possibility is a powerful spirit from the Avatar world that has been corrupted by the introduction of Naruto - like powers. This spirit could resent the intrusion of this new power source and seek to destroy anyone associated with it. It might have unique abilities that combine the spiritual magic of the Avatar world with the raw power of Naruto's chakra, making it a formidable foe.
Perhaps a dark entity from another dimension. This entity senses Naruto's powerful bloodline and wants to possess him or use his body as a vessel to enter the Naruto's world and wreak havoc. It would have otherworldly powers that Naruto has never faced before, making it a truly formidable antagonist.
It could be a combination of Orochimaru and Lex Luthor. Orochimaru from the Naruto universe is always seeking power and Lex Luthor from the DC universe is a brilliant but evil mastermind. They could team up, with Orochimaru being interested in Superman - like Naruto's unique physiology and Lex Luthor wanting to use Naruto's power to take over both the Naruto world and the DC world. They would be a formidable duo, constantly devising plans to undermine Naruto and his friends.
Perhaps it's a rogue Shinigami who doesn't want Naruto to figure out how to control his new form. This Shinigami might fear that Naruto could disrupt the balance between Hollows and Shinigami if he becomes too powerful in his hollow state. So, he tries to stop Naruto at every turn, creating a lot of conflict in the fanfiction.
It could be a powerful ninja from an ancient clan who sees the character with the godlike multi - bloodline as a threat to their own clan's supremacy. This antagonist would be very skilled in traditional ninja arts and would use their knowledge of the old ways to try and defeat the protagonist.
It could be Orochimaru from the Naruto universe who somehow manages to infiltrate the Metal Gear world. With his knowledge of dark jutsus and his devious nature, he would make a great antagonist. He could start experimenting on the soldiers in the Metal Gear world, creating some sort of mutant - ninja - soldier hybrids.
It could be a powerful dragon who has been corrupted by dark magic. This dragon might see Naruto's newfound powers as a threat and decides to target him and the Hidden Leaf Village first.
Maybe an ancient being that was sealed away long ago in the RWBY world but has now been awakened by Naruto's arrival. This being, with its own set of dark powers, sees Naruto as a threat to its plans of domination. It starts to create chaos, summoning Grimm in large numbers and using some form of corrupted chakra - like energy to attack. The RWBY characters and Naruto would have to put aside their differences and combine their skills to defeat this powerful foe.
Perhaps it's an old enemy who has somehow managed to come back stronger. Maybe someone from Orochimaru's old experiments that went wrong, but instead of dying, they gained some dark and powerful abilities. They see Naruto's return as a threat to their plans of world domination, so they target Konoha first. They might be able to control dark chakra in a way that no one has seen before, and use it to create chaos and destruction. They could also have some minions who are equally as powerful and loyal to them, making them a formidable foe for Naruto and Konoha.