A great plot could be that Naruto, with his smart thinking, discovers a hidden power within Sakura that she was unaware of. He then helps her to unlock and control this power. This journey of discovery brings them closer together as they have to rely on each other. They might have to go on a quest to find the final piece of the puzzle to fully unlock Sakura's power, facing many enemies and obstacles along the way.
Maybe Naruto's intelligence allows him to come up with a new training regime for himself and Sakura. He devises a plan that not only enhances their physical abilities but also their emotional bond. They could face challenges during this training that test their relationship and skills, like a sudden attack from a group of rogue ninjas while they are in the middle of a difficult exercise.
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.
A possible plot is that Naruto, being smart, figures out a way to upgrade the Hyuga clan's Gentle Fist technique. He shares this with Hinata, and they train together to perfect it. This not only strengthens their bond but also makes Hinata a more formidable ninja. Or perhaps Naruto uses his intelligence to find a cure for an illness that is affecting Hinata's family member. As they search for the cure, they grow closer and their relationship deepens.
Perhaps Naruto's intelligence allows him to discover a new form of jutsu related to the mind, which Ino is naturally interested in. They collaborate to perfect this jutsu, spending long hours together in research and practice. During this time, they start to see each other in a different light. Their friendship evolves into a romantic relationship, and they face challenges from those who oppose their new jutsu's development.
Another plot idea is that Naruto, Sakura, and Ino are transported to a different dimension. In this dimension, they have to find a way back home while also dealing with the new and strange rules. They meet different versions of themselves and their friends. This makes them question their identities and relationships. Along the way, they have to combine their powers and wits to overcome the challenges and find their way back to their own world.
A plot could involve a time - travel aspect. Naruto, Ino, and Sakura are sent back in time to their early days at the academy. They use their future knowledge to change some events, and in the process, their relationships develop in different ways. Naruto could see Ino and Sakura in a new light as they all struggle to keep their time - traveling a secret and deal with the changes they're making to the past. This could lead to a complex web of emotions and relationships between the three.
Maybe a story where an enemy targets Sarada to get to Naruto and Sakura. Naruto and Sakura then have to put aside all their differences and past issues to protect their daughter. This could involve flashbacks to their own relationship history and how they overcame obstacles in the past. It could also show Sarada realizing the depth of her parents' love for each other and for her.
Maybe in a fanfiction, there is a threat to the entire ninja world that requires the unique skills of both Gaara and Sakura. They are forced to train together intensively. During this time, Sakura discovers Gaara's softer side that he usually hides, and Gaara is impressed by Sakura's determination and medical skills. This leads to a deep emotional connection between them.
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 story where Naruto has to go on a mission with Hinata, Sakura and Ino. During the mission, they face various challenges that test their skills and teamwork. Hinata might use her Byakugan to detect hidden enemies, Sakura could heal any injuries, and Ino might use her mind - transfer jutsu for intelligence gathering. This would strengthen their bond and also lead to some character development among them.
One plot idea could be that in a world where Sakura is male, he and Naruto are on a mission together and get trapped in a cave. During their time there, they start to open up about their insecurities and feelings for each other, leading to a deeper bond. Another could be that male Sakura is a medic nin who has to take care of an injured Naruto after a battle. As he nurses Naruto back to health, they realize their feelings have changed. A third idea is that they are both entered in a ninja tournament and as they compete against others and support each other, a romantic relationship begins to form.
Maybe in the fanfiction, a smart Luffy figures out a way to read Poneglyphs with Robin's help. This new ability draws the attention of both the World Government and other pirate crews. They then have to go on a journey to protect this new - found knowledge while also using it to uncover more secrets about the Void Century.