Perhaps there is a prophecy that a union between them would result in a special child. They initially resist the idea but as the pregnancy progresses, they start to embrace the new situation and work together to protect the unborn child from those who might want to harm it. They also have to face the challenges of changing their relationship from rivals to co - parents.
One idea could be that they face challenges from the ninja world due to their relationship. People might be against a Uzumaki and a Uchiha having a child together. Another could be that Sasuke discovers new powers during her pregnancy related to the Uchiha heritage. For example, her Sharingan could develop a new ability to protect the unborn child.
A plot idea could be that there is some sort of threat to the pregnancy. Maybe an old enemy of either Naruto or Sasuke resurfaces and tries to target the unborn child. This would lead to them having to go into hiding and rely on their closest friends for protection. Or perhaps they discover some unique ninja ability that the baby might inherit, and they have to figure out how to nurture that ability even before the baby is born.
A possible plot is that the pregnancy is a result of some sort of chakra - related phenomenon. This causes some concerns among the medical ninjas in the village. Naruto and Sasuke have to deal with the mystery behind it while also preparing for their new family member. They might have to travel to different places to seek answers, all while Sasuke is dealing with the physical and emotional changes of pregnancy.
One plot idea could be that they face challenges from their respective villages due to their relationship. Since Naruto is from Konoha and Sasuke (even as a female in this fanfiction) has a complex history with the village. Another idea is that they go on a journey to find a safe place to raise their child away from the shinobi world's politics. Maybe they discover new jutsus during this time that they can pass on to their baby in the future.
One idea could be that Sasuke and Naruko are on a mission together when they find out about the pregnancy. This unexpected news forces them to re - evaluate their ninja lives and how they will protect their future family while still fulfilling their duties to the village.
One idea could be that they have to face the challenges of being pregnant in a world full of shinobi battles. Maybe they have to hide their pregnancies from enemies who might see it as a weakness. Another could be that they support each other through the physical and emotional changes, and their friendship grows even deeper during this time.
One idea could be exploring how Naruto's friends react to his pregnancy. They might be shocked at first but then become very protective. Another could be how Naruto copes with the physical and emotional changes during pregnancy while still being a ninja.
How about a story where an unknown enemy creates clones of them? Naruto, Sasuke, and Sakura have to not only fight these clones but also figure out who the enemy is and why they are being targeted. Along the way, they might discover new powers within themselves and also learn more about their relationships with each other.
One idea could be that as twins, they discover a hidden power that only they can access together. Maybe it's a special jutsu passed down in their family that requires their combined efforts. For example, they might be able to open a portal to a secret dimension filled with ancient ninja knowledge and powerful artifacts.
One idea could be that Naruto and Sasuke discover a hidden ancient jutsu that grants them immortality. They then use this newfound power to protect the ninja world from threats that are beyond normal shinobi capabilities. For example, they might face off against an otherworldly demon that is immune to normal attacks.