Perhaps a fanfic where an enemy uses smart genetic engineering in a cruel way. They create powerful and uncontrollable beasts that target the civilians of the Hidden Leaf. The enemy then uses their intelligence to avoid detection while these beasts wreak havoc. This not only causes physical harm but also spreads fear and chaos among the villagers, and the Leaf ninjas have to find a way to stop this cruel plot.
One idea could be a fanfic where a smart villain uses cruel tactics to undermine the Hidden Leaf Village. They might manipulate intel and set traps that are not only physically dangerous but also psychologically cruel to the ninjas. For example, making them doubt their comrades.
Perhaps Naruto, being smart, figures out a way to train with Sasuke in a new and unique way. They combine their skills in a way that no one has thought of before, leading to them both becoming even stronger and also deepening their bond. This could involve Naruto using his intelligence to analyze Sasuke's fighting style and find complementary techniques.
One idea could be a Naruto fanfic where Naruto himself becomes uncaring due to some great betrayal in the village. He still uses his smart strategic mind in battles but has no emotional attachment to his comrades or the village's cause. For example, he might use his knowledge of jutsu and the ninja world to simply survive and make his own path, without considering the traditional bonds of the ninja.
Another plot idea is to create an alternate universe where Jude and Cardan are forced to work together from the very beginning to stop a greater threat to Faerie. This would change the dynamics of their relationship and the overall story.
One idea could be that Bart discovers a hidden intelligence within himself and uses it to outwit the bullies at school. He could start solving complex math problems that even the teachers are amazed by.
Orochimaru is a character that can be easily written as smart and cruel in a fanfic. He is already known for his unethical experiments and his cunning nature. He could be made even more cruel in a fanfic, for example, by using his intelligence to create more deadly jutsus that he tests on innocent people without remorse.
One idea could be a time - travel fanfic where Naruto or Sasuke go back in time and try to change certain events. This would allow for a lot of creative storytelling as they interact with their younger selves and try to prevent future tragedies.
One idea could be to create an alternate universe where Naruto has a different elemental affinity from the start. For example, instead of wind, he has lightning. Another could be a fanfic focused on the relationships between the characters outside of the main plot, like how Sakura and Ino rekindle their friendship in a more in - depth way. Or you could write about Naruto's training journey with a different mentor, say Jiraiya's long - lost brother who has a completely different teaching style.
One idea could be a fanfic where Naruto travels to a different dimension where the Akatsuki are the heroes. Another could be a story about Naruto's kids growing up in a world where there's a new threat that they have to face without their parents' immediate help. And a third idea is a fanfic where Naruto discovers a hidden bloodline within himself that gives him unique powers.
One idea could be Naruto using his smarts and newfound powerful abilities to protect his harem from a powerful new enemy. For example, he could outwit the enemy by creating complex battle strategies and then use his enhanced power to execute them. Another plot idea might be Naruto teaching his harem members his unique skills, which in turn helps them become stronger as a group.
One idea could be Naruto using his newfound smarts to solve a mystery in the village that also involves Sakura. For example, he might figure out a way to stop a strange illness affecting the villagers and Sakura helps with her medical skills. Along the way, they grow closer.