Perhaps some of the other ninja villages see Naruto as a potential danger in the future, so they manage to infiltrate Konoha and make it seem like Naruto has committed a great crime, resulting in him being left in the forest. In this case, the main antagonist would be the ninja from the other villages.
Another possibility is that there's a new, unknown group within Konoha that wants to get rid of Naruto for their own purposes. They might be power - hungry individuals who think Naruto is getting too much attention and resources, so they scheme to have him left in the forest. So the main antagonist would be this secret group within Konoha.
In such a fanfic, perhaps Naruto is betrayed by his village and left in the forest. Maybe there are enemies lurking in the forest that he has to face alone. It could also involve Naruto's struggle to survive and his journey to find out why he was abandoned like this.
Danzo could be the main villain. He is known for his underhanded tactics and his dislike for Naruto. He might see Naruto as a threat to his power and plan to get rid of him by leaving him in the Forest of Death. Danzo could have manipulated some other characters to make it seem like it was a legitimate mission gone wrong.
Obviously, Naruto would be one of the main characters. Depending on the specific plot, Sasuke could also be involved. He might be one of the ones who either helps Naruto or is part of the reason Naruto is left to die. Sakura could also play a role, maybe she has a change of heart towards Naruto in the fanfic.
It could be someone who took advantage of Kushina's leaving. Maybe a rogue ninja who wants to use Naruto's vulnerability to their advantage. They could try to turn Naruto against the village by making him believe that the village drove Kushina away.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone who opposes Naruto's newfound admiration for Ganondorf. Maybe a traditionalist ninja who thinks Naruto is straying from the true ninja path by getting influenced by Ganondorf.
Lex Luthor could be a great antagonist. He's always looking for power and knowledge. If he discovers Naruto's abilities, he might try to use them for his own gain or see Naruto as a threat to his plans in Smallville.
It could be Orochimaru. He's always been interested in unique powers and abilities. The idea of X - 23's mutant abilities and Naruto's jinchuriki powers would be very appealing to him. He might try to capture them both to use in his experiments to gain ultimate power.