Perhaps a corrupted version of one of Naruto's comrades who has been influenced by the dark powers of Lucifer's world. This character would know all of Naruto's weaknesses and use them against him. At the same time, they would also have new demonic abilities, making them a formidable foe for both Naruto and Lucifer.
In a Naruto x Lucifer crossover fanfiction, the plot could start with a rift opening between the Naruto universe and Lucifer's world. Naruto, always eager to explore and help, enters the new world. There, he meets Lucifer. Lucifer is initially skeptical of Naruto but soon realizes his strength. They could then form an alliance. Naruto could teach Lucifer about friendship and loyalty, while Lucifer could introduce Naruto to the darker aspects of power and how to navigate them. Their combined forces would be a force to be reckoned with against any threats to either world.
It could be an evil ninja who has learned to use dark magic and wants to take over Pixie Hollow for its magic. He sees the fairies' magic as a source of power to enhance his own dark jutsu.
Another option could be Kabuto. He has been influenced by Orochimaru and is always looking for ways to gain more power. He might target Kurenai to learn more about her genjutsu and Naruto because of his status as a hero. Kabuto could be plotting to use their powers to further his own goals in the ninja world.
Perhaps it could be a character who is jealous of both Naruto and Hercules. A sorcerer who was once shunned in both worlds and now wants to prove himself by defeating them. He could use dark magic to create chaos and try to stop Naruto and Hercules from uniting and using their combined powers.
It could be Bowser who has somehow gained the power of a powerful ninja jutsu. He uses this new - found power to take over both the Mushroom Kingdom and start invading the Naruto world. His fire - breathing ability combined with ninja techniques would make him a formidable foe for Naruto and Mario.
It could be Orochimaru. Imagine he discovers the power of the ocean in Moana's world and wants to use it for his own dark experiments. He could start corrupting the sea creatures and causing chaos on Moana's island. Naruto, having faced Orochimaru before, would know his weaknesses and team up with Moana to stop him.
It could be Orochimaru. He might be interested in Tenten's unique weapon skills and Naruto's power of the Nine - Tails. He could try to capture them to conduct experiments on how to combine their powers for his own gain. He might create some sort of hybrid - clone with Tenten's weapon - using abilities and Naruto's chakra.
Perhaps a new character could be created as the main villain. This character could be an ancient being that was sealed away long ago and is now awakened by the interference of both Naruto's and Indiana Jones' worlds. The villain would be interested in using the unique aspects of both worlds, like Naruto's chakra and Indiana's artifacts, to reshape the universe according to his own desires. He would be extremely powerful, having abilities that neither Naruto nor Indiana has faced before, and would require them to combine their skills and knowledge in order to defeat him.
It could be a combined villain. For example, Orochimaru from the Naruto universe teams up with a powerful magic - user from Wanda's world who is jealous of Wanda's powers. This villain duo could be really menacing as they combine Orochimaru's dark jutsu and the magic - user's powerful spells.
A fallen angel who is jealous of Lucifer's newfound friendship with Supergirl and his life on Earth. This fallen angel decides to cause destruction on Earth to get back at Lucifer and also sees Supergirl as a threat to his plans of ruling over the mortals.