One plot idea could be that Naruto and Wonder Woman are brought together by a powerful villain who is causing chaos in both their worlds. They have to combine their unique skills, Naruto's ninja techniques and Wonder Woman's superpowers, to defeat the villain. Another could be a story where Naruto is accidentally transported to Wonder Woman's universe and he has to learn the ways of this new world while also helping Wonder Woman with a local threat.
Well, a plot could involve a magical artifact that has the power to destroy both universes. Naruto and Wonder Woman are the only ones who can find and protect it. Along the way, they face many challenges, like Wonder Woman having to deal with Naruto's sometimes reckless ninja ways and Naruto having to adapt to Wonder Woman's more diplomatic approach. As they journey, they develop a deep friendship and respect for each other's abilities.