A possible plot could involve a mystery within the village. Naruto, being smarter, is the first to piece together the clues and solve the mystery. Shikamaru, who usually excels in such situations, is left playing catch - up. Naruto could use his intelligence to not only solve the mystery but also prevent a greater disaster from befalling the village, showing that his intelligence is a valuable asset to the community.
In the Naruto series, Shikamaru is often seen as a highly intelligent character. However, in a fanfic where Naruto is considered smarter, it could be interesting. Maybe Naruto's quick thinking in battles, his ability to come up with unique strategies on the fly, is emphasized more. For example, in the original series, Naruto has his own way of solving problems that doesn't always follow the traditional 'smart' way like Shikamaru. But in this fanfic, his intelligence might be shown in more academic or strategic areas that were previously dominated by Shikamaru's perception of intelligence.
Perhaps in the fanfic, Harry is smart in ways that are not recognized by the wizarding world's traditional measures. He might have an in - depth understanding of magic that goes beyond what he shows in school. Maybe he's secretly researching ancient spells and magic theories that could be used to solve bigger problems in the wizarding community, but he doesn't want to draw attention to himself until he's fully prepared.
Perhaps Shikamaru has made a decision that deeply affects Naruto. For example, Shikamaru might choose to leave the village for a dangerous solo mission. Naruto, who values their friendship, cries because he's worried about Shikamaru's safety and the thought of losing his friend. In the fanfic, this could lead to Naruto trying to convince Shikamaru to change his mind.
The plot might also focus on their daily lives in the village. They could be shown hanging out, sharing their dreams and fears. Naruto might talk about his goal to become Hokage and Shikamaru could share his concerns about the responsibilities that come with being in the shinobi world. They could also get into friendly competitions like a race across the rooftops of the village, with Naruto using his speed and Shikamaru using his intelligence to find shortcuts.
One possible plot could be that Naruto and Shikamaru are on opposing sides in a strategic battle. Naruto might be brash and ready to go all - out, while Shikamaru is using his intelligence to outwit Naruto. Maybe it's a sparring match within the Hidden Leaf village where they have different goals. Naruto could be aiming to prove his strength, and Shikamaru is trying to show that brains can overpower brawn. They might start with some basic jutsu exchanges, and as the fight progresses, Naruto realizes he needs to use more than just his raw power to defeat Shikamaru.
Maybe Harry discovers a new form of magic that Hermione has overlooked, and he uses it to solve a major problem in the wizarding world. This makes him seem smarter in that aspect.
In a 'Naruto marries Shikamaru' fanfiction, the plot might involve Naruto being a bit lost after all the chaos of saving the village. Shikamaru, being the perceptive one, helps him through it. They bond over their shared experiences of growing up in Konoha. As they spend more time together, the village elders might oppose their relationship at first, but Naruto and Shikamaru prove that their love can overcome any obstacle. And they finally get married in a big ceremony with all their friends from the village in attendance.
One possible plot could be that they go on a mission together. Shikamaru's strategic mind and Temari's powerful wind jutsu would make them a great team. They might face a powerful enemy that requires both their skills to defeat. Along the way, they start to understand each other more deeply and their relationship begins to develop into something more than just comrades.
One possible plot could be that Mikoto somehow survived and she takes Naruto under her wing. She trains him secretly, using her Uchiha knowledge to make him stronger. This could lead to Naruto having a unique set of skills that no one else has.
Well, one possibility is that Naruto resigns due to feeling burnt out from all the battles and political unrest in the village. He might decide he's done his part and wants a simple life away from the chaos.