Madara Uchiha could also be a great main antagonist in this type of fanfiction. Imagine if he was resurrected in a way that incorporated the dark energy from Dark Nights Metal. His already powerful Sharingan abilities could be enhanced to a terrifying level, and his goals of creating a new world order could be even more extreme and dangerous.
A new character could be introduced as the main antagonist. This character could be a being from the Dark Nights Metal universe who somehow finds its way into the Naruto world. It could possess incredible powers, like the ability to manipulate the very fabric of the Ninja World's reality, and it would see Naruto and his friends as obstacles to its own dark plans.
It could be Orochimaru. He's always been interested in dark and forbidden jutsu. In this fanfiction, he might have found a way to merge the dark forces of Dark Nights Metal with his own research, becoming an even more powerful and menacing antagonist.
It could involve Naruto characters in a dark, alternate universe inspired by the Dark Nights Metal concept. Maybe Naruto has to face an even more corrupted version of the Akatsuki, with powers twisted by the dark forces from that concept.
It could be an old enemy of the Hidden Leaf Village who has a vendetta against the village for some past wrong. This antagonist could be a powerful ninja who also has his own set of metal claws, but his are corrupted with dark chakra. He wants to steal Naruto's claws, believing that they hold the key to ultimate power, and will stop at nothing to get them.
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 an unknown ninja who has been secretly studying dark energon for years. He wants to use it to take over the ninja world, believing that the power of dark energon will make him invincible.
It could be a rogue Dark Jedi who has escaped from his own Order and sees the Naruto world as a new place to spread chaos. He might be seeking powerful chakra sources to fuel his Dark Side powers.
It could be Sasuke. If Sasuke continues to pursue his own vendetta in a more extreme way and Naruto's attempts to bring him back fail, Sasuke could become the main antagonist. Their rivalry could turn into a full - blown battle for power and ideology, with Naruto being pushed to his limits and potentially turning dark in the process of trying to stop Sasuke.
Batman is one of the main characters. He's the one who discovers the secrets of the Dark Multiverse. Superman and Wonder Woman are also main characters as they are part of the heroes who fight against the threats from the Dark Multiverse.
It could be the leader of the dark guild. This person would likely have a very different ideology from Naruto's. Maybe the leader believes in using extreme and unethical means to gain power, like sacrificing innocent lives for dark magic. Naruto would constantly clash with this leader as he tries to uphold his own values.
It could be a long - lost moon - dwelling ninja clan that has a grudge against the Leaf Village. They see Naruto as a threat to their plans on the moon's dark side.
It could be a rogue ninja who is also after the power of the chakra chains. This ninja might see Naruto as a threat and try to eliminate him to get the chains for himself.