Maybe it's a rogue member of a powerful ninja clan. This person has been exiled for their unethical experiments with dark forces. They discover dark energon and see it as a chance to get revenge on their clan and the entire ninja world. So they start using it to create powerful and dark creatures to do their bidding.
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.
Well, it could be about Naruto finding a dark energon source in the Hidden Leaf Village. Maybe it starts to corrupt the villagers, and Naruto has to find a way to stop its spread while also dealing with the changes in his friends who are affected by it.
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.
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 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 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.
Perhaps an old member of a forgotten clan who was exiled because of his dark blood. He returns with a vendetta against the village that shunned him. He sees Naruto as a symbol of everything he hates and tries to destroy him. The main antagonist could also manipulate other ninja to turn against Naruto by spreading fear about his dark blood.
Perhaps a group of dark side cultists could be the main antagonists. They idolize the power of the dark side and see Ahsoka as a prime candidate to join their ranks. When she refuses at first, they start to hunt her down, but in the process, they unknowingly push her closer to the dark side, creating a complex dynamic where they are both the pursuers and the inadvertent cause of her fall to the dark side.
The Green Goblin could be a great main antagonist in a dark fanfiction. He could be even more deranged and have a more elaborate plan to destroy Spider - Man, not just physically but also mentally by targeting his relationships.