One idea could be a story where Naruto and his clone have to work together to overcome a unique training challenge. They learn to combine their skills in new ways, like one using a shadow clone to distract while the other performs a powerful jutsu. This focuses on their growth and teamwork without any inappropriate content.
Perhaps they could embark on a journey to find a rare ingredient for a special medicine. Along the way, they encounter various characters from the Naruto universe and have to use their wits and ninja skills. The clone could provide an extra set of hands and a different perspective, leading to an exciting adventure story.