It could be an organization of rogue ninja who have also somehow gained similar powers but use them for destruction. They see Naruto as a threat to their plans of taking over the ninja world with their newfound powers. They constantly try to undermine Naruto and steal his unique Crystal Dragon Slayer techniques.
It could be a rogue ninja who has also somehow gained crystal dragon slayer powers but uses them for evil. He might be jealous of Naruto's natural talent and popularity, so he tries to destroy Naruto and take over the ninja world using his newfound powers.
One possible plot could be Naruto discovers he has the power of a Crystal Dragon Slayer. He might use this power to fight against new and powerful enemies in the Naruto universe. Maybe he has to protect his village from a threat that only his unique abilities can counter.
It could be a powerful dark wizard who sees Natsu as a threat because of his alpha status among dragon slayers. This wizard might want to eliminate Natsu to gain control over the dragon slayers or to carry out some evil plan without interference.
There might also be some dark magic - using villains who want to use Natsu's alpha dragon slayer powers for their own evil purposes. They could try to capture him or manipulate him in some way. Maybe they plan to extract his power to create a powerful weapon or something.
It could be powerful fairies who have a vendetta against Lucy for being a slayer. Maybe they are the leaders of a fairy clan who see her as a threat to their existence.
It could be an existing character like Naruto who, through some strange turn of events, gains the Wood Dragon Slayer power. This would completely change his fighting style and how he approaches challenges. He could use the power in creative ways, like combining it with his Rasengan to create a new, more powerful attack.
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.
It could be an evil shinobi who has somehow harnessed shadow dragon slayer magic for his own evil purposes. He uses it to create chaos and destruction in the ninja world, and Naruto and the dragon slayer have to stop him.
There could be a secret organization that believes the golden dragons are the key to a new world order. They oppose Naruto's attempts to slay the dragons because they want to harness their power for their own, often evil, purposes. They might send their most powerful assassins after Naruto to stop him.
Maybe Akainu from One Piece (in a crossover sense within the fanfiction). He could be warped into this Naruto - Dragon Slayer world and his extreme sense of justice could be twisted into a form of tyranny. He sees the chaos and magic in this new world as a threat that needs to be eliminated, and in his overzealousness, he becomes the main antagonist, causing destruction and pitting the ninjas and dragon slayers against him.