A more complex fanfiction could involve a merging of the two universes. Characters from both Naruto and Wonder Woman start to have similar powers. For example, Naruto could gain some of Wonder Woman's powers like the ability to fly or enhanced strength. In return, Wonder Woman could learn to control chakra. This would create a whole new dynamic in the story as they all adapt to these changes.
Another idea is a story where Wonder Woman visits the Naruto universe. She could learn about chakra and ninjutsu. Maybe she helps the ninja villages come together in a time of great crisis, using her wisdom and strength. She might also be intrigued by the concept of the tailed beasts and try to understand their power.
One idea could be a crossover where Naruto is somehow transported to the Young Justice universe and teams up with the heroes there, and then they encounter Wonder Woman. Maybe Naruto's unique jutsu skills can be used in a joint mission with the Young Justice team's powers and Wonder Woman's abilities.
A great fanfiction concept could involve a magical accident that transports Marinette (Ladybug) to the world of Wonder Woman. There, she has to learn to adapt to the new environment while also helping Wonder Woman deal with a threat that only Ladybug's unique powers can assist with. For example, a villain who can create illusions that are so powerful, only Ladybug's Lucky Charm can break through them. And in the process, Marinette discovers new aspects of her own powers.
Another concept is that Naruto is sent to Middle - earth. There, he could use his ninja skills and chakra powers. He and Gandalf could team up to fight Sauron. Naruto's ability to make friends and inspire others would be really useful in uniting the different races of Middle - earth against the common enemy.
A more complex idea is that the Matrix is used to create a virtual training ground for the shinobi. They enter the Matrix to practice their skills in a more controlled environment. However, they soon realize that there are some dark secrets within the Matrix, and Naruto has to lead the way to uncover the truth and free those who are trapped inside.
Another possibility is that Naruto visits the Townsville, the city where the PPG live. He might be confused by the modern technology there compared to his own world. The PPG could teach him about it while he shows them some of his ninja skills like tree - climbing and water - walking.
A third idea could be a story where Naruto's clones are mistaken for some kind of superpower by the Thundermans. Max might be intrigued and try to figure out how to do it himself. Meanwhile, the Thundermans could teach Naruto about modern technology which he has never seen in his own world. This could lead to some really interesting and comical situations as they try to understand each other's worlds.
Another possibility is that Pokemon exist in the Naruto world. Some ninja could have Pokemon as partners instead of traditional ninja animals. For example, Sasuke could have a Dark - type Pokemon like Umbreon that would match his cool and mysterious personality. And the Pokemon battles could be incorporated into the ninja battles, adding a new layer of strategy.
One idea could be a crossover where Naruto characters gain the abilities of Needless characters. For example, Naruto could get the power of Adam Blade's regeneration. It would be interesting to see how he uses it in battle, especially against tough foes like Pain or Madara.
Another concept could be a fusion of their powers. Imagine if Naruto was somehow able to absorb Frieza's power or vice versa. This could create a new and extremely powerful being. The story could explore how this new entity would interact with the two different universes. Would it be a force for good or would the power corrupt it? There could be a lot of internal conflict as the combined Naruto - Frieza entity struggles with its new identity and purpose.
Another possibility is that Godzilla somehow ends up in the Naruto world. The shinobi might initially see it as a great threat, but Naruto could try to communicate with it using his ability to sense emotions. Maybe Godzilla is there because it's being chased by an even greater enemy from its own world, and Naruto and his friends decide to help it.