Maybe in the fanfiction, a strange disease has made it difficult for people to have children. Naruto discovers a new form of chakra - based medicine that can reverse this. He then travels around the world, teaching others how to use this medicine and also promoting the idea of having more children. This could lead to different adventures as he faces opposition from some who don't believe in his methods.
It could be that Naruto finds a hidden ancient jutsu that has the power to repopulate the world. However, this jutsu has some risks associated with it. Naruto has to balance the need to use it to increase the population with the potential negative consequences. Along the way, he gets help from his friends like Sasuke and Sakura, who each contribute their own skills and ideas to make the plan work.
Sakura would be a likely main character. She is a skilled medical ninja, so she could play a crucial role in ensuring the health of those involved in the repopulation efforts. For example, she could develop new medical procedures to help with childbirth or deal with any potential health issues that might arise during pregnancy.
One possible plot idea could be Naruto finding himself in a world where most of the important roles are taken by females. He could struggle to adapt to this new dynamic at first. For example, the Hokage could be a female and have different leadership styles. Naruto would then have to prove himself in this female - dominated society, perhaps by using his unique skills in new ways to gain respect.
In some Naruto repopulate fanfictions, a plot could be centered around Naruto himself starting a family as a symbol for others to follow. He might face challenges like finding the right partner who can support his role in leading the repopulation effort. Or perhaps a group of ninjas from different villages form a pact to repopulate the ninja world after a major disaster that depleted their numbers. They would have to overcome cultural differences and past rivalries. Also, there could be a plot where a new threat emerges, and the only way to combat it is by increasing the population of strong ninjas, so Naruto and his friends have to figure out how to make that happen.
One possible plot idea could be that Naruto somehow gets transported to the Estrossa world and has to adapt to its rules and powers. He might have to learn new jutsus or abilities based on the Estrossa system.
One possible plot could be Naruto meets Scorpion and they end up having to team up against a common enemy. Maybe an organization that threatens both the Hidden Leaf Village and Scorpion's interests. Naruto's positive attitude starts to rub off on Scorpion, making him question his own dark past and motives.
One idea could be a modern - day person suddenly being transported into the Naruto world and having to learn chakra control from scratch. They could struggle with the cultural differences and make friends with some of the original characters like Naruto or Sakura while trying to find a way back home.
The plot could be that the baby gets lost in a mysterious part of the ninja world. Naruto and Sakura go on a search mission to find their baby. Along the way, they discover new secrets about the ninja world and also learn more about themselves as parents. They face various challenges and meet different characters who either help or hinder their search.
He might write about his own journey from an outcast in the village to a hero. Maybe he'd include details about his training with Jiraiya that were never fully told. He could also write about his relationships with Sasuke and Sakura in a more in - depth way, exploring their growth together and apart.
One plot idea could be that Naruto, during his adventures, meets Tayuya in a different context than in the original story. Maybe he saves her from some danger and then gradually falls in love with her as he discovers her true self.
One plot idea could be Naruto time - traveling back to Hashirama's era and learning from him directly. This could lead to Naruto bringing back some forgotten knowledge or skills to his own time.