In a fanfiction like this, it could be that a powerful and unknown force outside the village frames Naruto and Shikamaru. The village elders, fearing for the safety of the village, banish them. They then embark on a journey to find the real culprits. Along the way, they learn new jutsus and skills from different people they meet, which they will use later to clear their names and protect the village from the real threat.
Perhaps there's a political conspiracy in the village. Naruto and Shikamaru discover some dark secrets that certain powerful people in the village don't want exposed. So, they are banished to keep them quiet. They then form an alliance with other outcasts and work towards uncovering the truth and returning to the village to set things right. This could involve a lot of action scenes as they fight off those sent to stop them.
In this fanfiction, Naruto and Kakashi are banished because of a prophecy that some in the village misinterpret. The prophecy seems to suggest they will bring doom, but in reality, it's about a different kind of change. While banished, they explore different lands, learn new jutsu from other ninja clans, and eventually return to the village stronger and wiser, proving the prophecy was misread.
In this fanfiction, Hinata could be badass in a way that she challenges the village elders directly about Naruto's banishment. She argues that Naruto has been the savior of the village multiple times and his banishment is unjust. As she does this, she also showcases her new and improved combat skills, which she has been secretly honing, to intimidate those who oppose her and show that she will fight for Naruto's return.
A possible plot is that Shikamaru is kidnapped by a rival village that believes his strategic mind can give them an edge in an upcoming war. His kidnappers try to brainwash him into working for them. However, Shikamaru uses his wits to resist and also leaves subtle clues for his comrades to find him. His friends, on the other hand, must infiltrate the rival village without getting caught to rescue him.
One plot idea could be that Naruto and Shikamaru are assigned a top - secret mission in the ANBU. They have to infiltrate a hidden enemy base. Naruto's brute strength and Shikamaru's intelligence would make for an interesting combination as they face various traps and strong opponents inside the base.
One idea could be that Naruto discovers a mute girl in a hidden village during one of his travels. Shikamaru gets involved as Naruto tries to find a way to communicate with her. Maybe she has a unique power that only she can use, but because she's mute, she has trouble expressing it. Naruto's determination and Shikamaru's intelligence work together to help her out.
Perhaps Naruto, in his banished state, has some new and unique abilities that Temari is intrigued by. She decides to help him master these powers in secret. As they train together, feelings start to develop. Their relationship could then be a source of conflict between Konoha and Suna as the two villages have different views on Naruto's banishment and his newfound connection with Temari.
One plot idea could be that Naruto, after being banished, crosses paths with Kurenai who is on a solo mission. She initially has her doubts about him due to his banishment but gradually realizes he was wrongly accused. They team up to face a common enemy that threatens the village from afar. This could lead to a growing bond between them.
One idea could be that Shikamaru and Temari have to go on a joint mission in a foreign land. They face various challenges together which make them rely on each other's skills. Shikamaru uses his intelligence to outwit the enemies while Temari uses her wind jutsu. This mission brings them closer and they start to develop deeper feelings for each other.
One idea could be a story where fem Naruto and Shikamaru are on a mission together in a mysterious forest. They encounter strange creatures and have to use their unique skills to survive. Fem Naruto could use her speed and agility, while Shikamaru uses his intelligence to strategize.
One plot idea could be that Naruto and Shikamaru's team is sent on a mission to a mysterious forest where they encounter a new and powerful type of ninja beast. They have to figure out how to defeat it without using their usual jutsu. Another idea is that their team is tasked with protecting a foreign dignitary who has a secret that could change the balance of power in the ninja world. They face many assassination attempts and have to work together to keep the dignitary alive.