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.