It could be a powerful spirit that is enraged by Naruto's soul - eating. This spirit might have been protecting the souls in the first place and now sees Naruto as a great threat.
It could be an evil ninja from Naruto's world who has somehow also gained access to the powers of the Beyond Two Souls world. This character could use these new powers to try and take over both worlds.
Obviously Naruto himself would be a main character, in his dark form. There might also be other characters like Sasuke. Sasuke might be in a position of either trying to stop Naruto or joining him in his dark deeds. And Sakura could also be there, perhaps as a voice of reason trying to bring Naruto back from the darkness.
Perhaps in the 'naruto eats souls fanfiction', Naruto is cursed by an evil force. This curse makes him uncontrollably eat souls. He then has to struggle to find a way to break the curse while dealing with the consequences of having eaten souls, like the anger of the spirits' friends or families.
The World Government could become the main antagonist. They would see Luffy's new power as a threat, especially if he starts using it in ways that oppose their rule. They might send out their strongest agents, like the Admirals, to take Luffy down. The Admirals could have developed new techniques to deal with the dark dark fruit powers, making them a formidable foe for Luffy.
Well, it could be about a dark version of Naruto having the power or the need to consume souls. Maybe it's a twisted take on his character where he's no longer the hero we know, but a being driven by some dark force to feed on souls for power or survival.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
Maybe a new character could be introduced as the main antagonist. This character could be from a hidden village that has been secretly observing Naruto's growth. They realize his potential as a weapon and plan to steal his power or use him to start a war against other villages.
Krampus himself could be the main antagonist. Since he is a figure known for punishing the naughty, his actions in the Naruto world might be seen as unjust. He could be going after ninjas without really understanding their motives, causing a lot of trouble for the main characters.
It could be a rogue ninja who also has somehow acquired bankai - like powers. This antagonist might be jealous of Naruto's newfound abilities and wants to prove that he is the stronger one. So he starts causing chaos in the ninja world, challenging Naruto at every turn.
It could be a rogue ninja who wants to disrupt Naruto's business to gain power. Maybe he's jealous of Naruto's success and popularity in the business world. He could try to steal Naruto's business secrets or sabotage his operations.