The relationships within the village would be severely affected. His friends would be heartbroken and split into groups, some trying to find him, others blaming themselves. The new generation of ninjas would also lack a role model. And the balance of power in the ninja world could shift, as other villages might see Konoha as weakened without Naruto and try to gain an upper hand.
The village would likely be in chaos. Naruto has been a key figure in protecting the Hidden Leaf. Without him, there would be a power vacuum, and enemies might see it as an opportunity to attack. The villagers who once relied on Naruto would be filled with fear and uncertainty.
One possible reason could be a mission. In many Naruto - related stories, missions often take characters away from their families. Naruto might have received a highly important and dangerous mission that requires him to be away from Kushina for a long time.
Maybe Naruto discovers that the village he has been trying so hard to protect has been using him all along. He might find out some dark secrets about the Hidden Leaf, like they were involved in something immoral and were just using his power, which would shatter his idealistic view of the village and leave him heartbroken.
Well, it could be due to the failure to protect the village. Naruto has always been about protecting Konoha. If something really bad happened, like a major attack that he couldn't prevent and many lives were lost, he might feel so much guilt and heartbreak that he decides to leave. He would feel like he failed his purpose.
One possible reason could be that Naruto feels he has learned all he can from Jiraiya at that point. Maybe he wants to explore his own path independently and test his skills without Jiraiya's constant guidance.
Well, in this 'Naruto gets Nibi pregnant' fanfiction idea, one consequence could be a huge scandal within the Hidden Leaf Village. Naruto is a respected figure, and such an unorthodox relationship would shock many. Also, from a genetic standpoint, we can only imagine the wild combination of Naruto's Uzumaki and Jinchuriki traits with the Nibi's feline - like and tailed - beast powers.
On the positive side, new and better policies could be implemented. If the old council was corrupt or stagnant, getting rid of them would open the door for fresh ideas and reforms. Naruto could bring in new people with different perspectives to help run the village, leading to a more prosperous and fair Konoha.
Sasuke could end up in a very dark place. He might get involved with some really bad characters or groups that could lead him further astray from his original path. He could lose his sense of self and become consumed by revenge or whatever negative emotions are driving him to leave in the first place.
In such a fanfiction, one possible consequence could be a major shift in the Naruto universe's social structure. With so many pregnancies, there would likely be a need to reevaluate how families are supported, and how the Hidden Villages would deal with a sudden population boom. It could also lead to complex relationship dynamics among the characters, as Naruto would have to handle his newfound responsibilities towards all these women and children.
If the fem Kyuubi gets control of Naruto in the fanfiction, one consequence could be that Naruto's relationships with his friends might be strained. His friends might not trust him anymore as they notice the change in his behavior under the Kyuubi's control. Another possibility is that Naruto could be used to cause chaos in the village. Since he's very powerful, the fem Kyuubi could use him to carry out her own plans, which might be harmful to the village and its people.