One plot idea could be that female Naruto discovers she's pregnant during a time of peace in the Hidden Leaf Village. She might struggle at first with the idea of being a mother while still having her ninja duties. She could then start to train in new ways that are less dangerous so she can protect her unborn child. Her friends, like Sakura, would be there to support her through the pregnancy, giving her medical advice and just being there for emotional support.
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.
One interesting plot could be baby Naruto and baby Sasuke getting lost in the forest together. They have to rely on their budding instincts and nascent chakra to find their way back. Maybe they encounter some small, friendly forest creatures that help them. Another idea is that they accidentally switch places in the village for a day. This leads to chaos as the villagers react differently to them being in the wrong 'homes'.
One idea could be that the baby is from a hidden clan. Naruto decides to protect the baby from those who would use its special abilities. He takes the baby under his wing and trains it as it grows up, passing on his ninja values.
One idea could be that Naruto is taken by a powerful but reclusive ninja who trains him in secret from a young age. This way, Naruto grows up with a different set of skills and a more focused mindset, perhaps even learning some ancient and forgotten jutsu. Another plot could involve Naruto being taken by a group of kind-hearted villagers from another village. They raise him as their own, and he grows up with a different view of the world outside of Konoha, which could lead to some interesting interactions when he eventually returns to Konoha.
Another plot could be that the baby gets lost in a mysterious ninja realm. Sakura and Naruto then have to embark on a dangerous journey to find their baby. Along the way, they face numerous challenges and also learn more about each other's love for their child and for each other.
One idea could be the Akatsuki members having to protect baby Naruto for some mysterious reason. Maybe they were tasked by a powerful entity to keep him safe from other dangerous forces in the Naruto universe.
One idea could be a story where baby Naruto somehow gets a vision of his father Minato's past battles. This would be really cool as Naruto could start showing early signs of his future strength inspired by his dad. Another plot could be Minato coming back briefly as a spirit to protect baby Naruto from some early threats that Kakashi or the Third Hokage might not be aware of.
One idea could be that Naruto and Sasuke find a baby on one of their missions. They then have to figure out how to take care of it while also dealing with the political implications in the ninja world. Maybe the baby has some special power that attracts the attention of both friends and foes.
Perhaps in this fanfiction, baby Sasuke and Naruto are accidentally sent to a parallel dimension. In this dimension, the ninja world is very different. They have to rely on each other more than ever to survive and find a way back home. Along the way, they meet alternate versions of their friends and foes.
One idea could be that baby Naruto somehow crosses paths with Itachi in a secret mission. Maybe Itachi is on a mission in Konoha and stumbles upon baby Naruto who has an unusual chakra flare. Itachi, being curious, decides to keep an eye on him without revealing himself. This could lead to a series of events where Itachi's actions unknowingly protect Naruto from some early threats.