Sarada could also be a main character. She is strong - willed and intelligent. She could be investigating a case of a missing - nin who is suspected of being involved in some sort of conspiracy against the Uchiha clan. This would give her a chance to show her detective skills and her loyalty to her clan.
Kawaki could be involved. He has his own dark past and understanding of the hardships. He might encounter a missing - nin who has a similar past of being used and discarded. Kawaki could then have to decide whether to show mercy or follow the rules regarding missing - nin.
One idea could be a missing - nin who was once a friend of Boruto's and has some unique jutsu. This missing - nin could be on a quest to find a cure for a rare disease that his family has. Boruto, upon learning of this, has to decide whether to bring him back as a missing - nin or help him.
In a 'boruto shinachiku world fanfic', potential characters would include Shinachiku's family members for sure. Naruto, being his father, would play an important role. Hinata as his mother would be there to support and guide him. Boruto would be his cool older brother. Besides, characters like Konohamaru, who is now a teacher, could also be in the story. He could train Shinachiku and help him grow as a ninja. Also, the friends that Shinachiku makes on his own adventures, new characters created specifically for the fanfic could be part of it.
Naruto is likely to be popular too. Even though it's a Boruto x Sasuke fanfic, Naruto's relationship with both of them is so important. He could play a role in supporting them from the sidelines or even getting involved in a crucial part of the story.
It could be the Kara organization. They've been shown to be interested in Boruto's Karma mark in the original series, so they might have finally made a move to abduct him in the fanfic.
Perhaps in this 'Boruto goes missing fanfic', Boruto is lured away by a mysterious figure who claims to have information about his future or his father Naruto's past. He follows this figure without thinking, only to find himself in a strange and dangerous place. His disappearance then sets off a chain of events in the village. People start to suspect that there might be a traitor among them who helped Boruto disappear. His teammates, like Sarada and Mitsuki, would then start their own investigation to find him, facing not only external threats but also internal doubts and suspicions within the village.
It could be a resurrected Orochimaru. He has always had an interest in power and the Akatsuki. He might return, more powerful than ever, and take control of the Akatsuki in the Boruto era, using them to carry out his evil plans, like creating an army of super - ninjas using some dark jutsu.
It could be a powerful and evil ninja from a rival village who has killed one of Boruto's close friends or family members.
There could also be an ancient evil that was sealed away long ago but is now awakened due to the changes in the ninja world. This evil force could possess people or create chaos in the villages. Boruto and Naruto would have to figure out how to stop it, perhaps by seeking out old allies and learning forgotten jutsu.
Naruto would be devastated. He might blame himself for not being able to protect his son. Sasuke would be angry and would likely go on a hunt for the perpetrator. His friends like Sarada and Mitsuki would be heartbroken. Sarada might vow to become stronger to prevent such a tragedy from happening again.
As I mentioned before, Boruto and Sarada are potential. Also, Cho - Cho and Shikadai could be a couple as they have a certain chemistry. They often interact in a way that hints at a possible romantic relationship in the future.