In a fanfiction, perhaps there's a mystery in the village that only Naruto, Dakura and Shikimaru can solve. It could involve a strange phenomenon that is affecting the chakra flow in certain areas. Naruto is eager to jump right in, Shikimaru is more cautious and tries to analyze the situation first, and Dakura has some knowledge about ancient lore that might be the key to solving the mystery.
A fanfiction could focus on a training arc. Dakura might be a new character in the village who is having trouble fitting in. Naruto and Shikimaru take it upon themselves to train Dakura. Naruto shows his energetic training methods, while Shikimaru teaches the more cerebral aspects of combat. Along the way, they learn about Dakura's past and the reasons for his insecurities.
Another relationship could be that of mentor and student. Shikimaru, with his intelligence, could be a mentor to Dakura in terms of strategic thinking. Naruto could also be a mentor in terms of building confidence and using chakra effectively. This would create a dynamic where Dakura is learning from two very different but equally important sources.
I haven't personally come across a Naruto fanfiction with this exact plot. It's possible it exists in the vast sea of fan - created stories, but it's not a common one that I'm aware of.
There's a fanfic called 'Teamwork Beyond Expectations'. In this story, Hinata, Naruto and Shikimaru are put in a situation where they have to rely on each other's skills. It's exciting to see how Naruto's impulsiveness, Hinata's kindness and Shikimaru's intelligence blend together. It really showcases the potential of their trio in different scenarios.
Another possibility is that Clayface somehow gets transported to the Naruto universe. The shinobi in the Naruto world would be very confused by his abilities. Clayface could try to blend in by mimicking the appearance of different shinobi, but his lack of chakra would give him away. Naruto might see through his disguise easily due to his own perceptive skills.
One idea could be a crossover where Naruto is transported to Noire's world. He could use his ninja skills to help Noire in her battles against the various threats in her realm. For example, Naruto's shadow clone jutsu could be used to confuse the enemies while Noire attacks from a different angle.
One idea could be a crossover where Naruto and his friends are transported to the Soul Society. Naruto's positive attitude and determination might inspire the Soul Reapers in a new way. He could learn some of their techniques, and in return, teach them about chakra and his own ninja skills.
A possible fanfiction plot is that Naruto has a strange dream about a powerful being named Yubel. Intrigued, he sets out on a journey to find out more about her. Along the way, he meets different characters who either know about Yubel or have some connection to the power she wields. This journey changes Naruto in ways he didn't expect, and he eventually finds a way to communicate with Yubel across different dimensions.
One idea could be a crossover where Naruto, with his ninja skills, is transported to Celty's world. He might team up with Celty to solve some mystery in her city. Naruto's ability to sense danger and Celty's unique skills could make for an interesting partnership.
A more comical fanfiction could be about Kale trying to adapt to the food in the Naruto world. Naruto could introduce her to ramen, and she might have some really funny reactions, while also sharing some Saiyan cuisine with Naruto and his friends.
One idea could be a story where Naruto somehow gains the ability to use Susanoo. Maybe through some strange chakra experiment gone wrong or a gift from an ancient entity. He then has to learn how to control this new power while still maintaining his own ninja way.