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.
Well, it might start with Indiana Jones stumbling upon some kind of ninja - related artifact that has a connection to Naruto's world. This could open a portal or something. Then, they could team up. Indiana could teach Naruto about the history and value of the artifacts they are after, while Naruto uses his chakra powers to fight off any supernatural threats that come their way. They could travel to different historical locations, both from Naruto's world like the Hidden Villages and from Indiana's world like ancient temples in South America.
Definitely Indiana Jones and Han Solo. Indiana's tenacity and knowledge of archaeology combined with Han's roguish charm and piloting skills would make for some great interactions. They could be on a quest for a valuable artifact that has significance in both the Star Wars galaxy and on Earth.
Lara Croft is very independent and strong - willed. Indiana Jones, while also confident, has a more laid - back charm. When they interact, there could be some initial friction. Lara might be a bit dismissive of Indiana's more old - school ways at first. But Indiana could be impressed by Lara's physical prowess. Eventually, they would learn to respect each other's skills and work together effectively.
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.
A possible plot could involve Lara Croft and Indiana Jones teaming up to find a lost ancient artifact. Maybe they start off as rivals, both after the same item. But as they face various traps and enemies in an ancient temple, they realize they need to work together. They could combine their unique skills, with Lara's acrobatic and combat abilities and Indiana's knowledge of archaeology and ancient cultures.
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.