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.
Danzo could also be a prime character for such a portrayal. He was always willing to make sacrifices and use underhanded means for what he believed was the good of the village. In a fanfic, his smartness could be shown in his elaborate political maneuvers, and his cruelty in the way he treats those who oppose him, like eliminating them quietly without a second thought.
Well, Naruto is likely to be one of the main characters since it's a 'naruto smart fanfic'. But there could also be his friends like Sasuke and Sakura. Sasuke might play a role in Naruto's journey of using his intelligence, perhaps as a rival who also respects Naruto's new - found smarts. Sakura could be there to support Naruto and use her own skills in combination with Naruto's intelligence, like in medical ninjutsu situations.
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.
It could be another ninja from a rival clan. For example, someone from the Hyuga clan who has a long - standing grudge against Sauske's clan.
Naruto can be shown as smart by having him solve complex puzzles or riddles. For example, he might come across an ancient ninja riddle that guards a powerful artifact. His ability to think outside the box and use his life experiences to figure out the answer would demonstrate his intelligence.
Maybe it was Jiraiya. Jiraiya was a very important figure in Naruto's life. He could have given Naruto the mask as part of a training exercise. He might have thought that wearing a mask would force Naruto to rely more on his intelligence rather than his brute strength in certain situations.
Definitely Naruto himself. In these fanfictions, he often takes on a more cerebral role, which is a refreshing take on his character. His ability to think on his feet and use his intelligence in various situations makes him stand out.
One possible plot could be that Naruto, being smart, quickly figures out a new and powerful jutsu. Sakura, impressed, decides to train with him more intensively. They go on a mission together where Naruto's newfound intelligence helps them outwit the enemy easily.
There could be an elder in the Smart Clan, like Master Kenji. He is highly respected for his vast knowledge and wisdom. He guides the younger members of the clan and often gets involved in important decisions regarding the clan's relationship with other clans and villages. Another main character might be a female ninja from the Smart Clan, say Ayumi. She is not only intelligent but also a skilled fighter, breaking the stereotype that the Smart Clan is only about brains.
Well, it depends on the specific fanfic. Some fanfics might really emphasize Naruto's growth to be on par with Minato in terms of smarts. They could show Naruto learning from Minato's memories or having some sort of spiritual connection that transfers knowledge. However, other fanfics might focus more on other aspects of Naruto's character and not necessarily make him as smart as Minato.
Perhaps Naruto wears the mask as a symbol of a new, more strategic side of himself. He could be using it to intimidate his opponents in battle. Since he's smart in this fanfic, he might have realized that a mysterious appearance can give him an edge. He could be using the mask to play mind games with his enemies, making them wonder who he really is and what his true capabilities are.