One possible plotline could be that Naruto discovers some long - lost secret about his mother Kushina and decides to leave the village with her to explore this mystery further. Maybe they are on a quest to find some hidden power or knowledge that is related to Kushina's Uzumaki heritage.
Another plot could be that Kushina is somehow brought back to life, and Naruto, longing for a family connection he never really had, leaves with her to start a new life away from the chaos and politics of the Hidden Leaf Village. They might go to a far - off land where they can live in peace and Kushina can teach Naruto things she never got the chance to before.
It could also be that there is a threat to Naruto's life in the village, and Kushina, in a spirit - like form, guides Naruto out of the village to keep him safe. Along the way, they have various adventures, and Naruto learns more about his mother's past and her relationship with the village, which changes his perspective on many things.
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.
One possible plotline could be that Naruto leaves with Tsunade on a mission to find a rare herb that is said to have the power to heal any wound. Along the way, they face various enemies who also want the herb for their own malicious purposes. Naruto's skills and Tsunade's wisdom would be put to the test as they battle their way through.
One possible plotline could be that Naruto is somehow transported back in time and has to fight Kushina in a misunderstanding. Maybe he's mistaken for an enemy due to some time - warp magic or jutsu gone wrong. Another could be a scenario where Kushina is controlled by an evil force, and Naruto has to fight her to break the control. Or perhaps it's a sparring match in a dream world where Naruto and Kushina test each other's skills without real harm.
One reason could be the motherly love. Kushina always loved Naruto deep down. Leaving him means missing out on his growth and important moments in his life. Another reason might be realizing the hardships Naruto faced without her presence. She probably feels guilty for not being there to protect him from the loneliness and the many challenges he had to endure in the village.
One possible plotline could be Naruto's struggle with abandonment issues. Since Kushina left, Naruto might have a harder time finding his place in the village. He could become more withdrawn and have to fight even harder to prove himself. Another could be the search for Kushina. Naruto might embark on a journey to find out why she left and try to bring her back.
One possible plotline could be that Naruto is somehow tricked into leaving with Kisami and Itachi. Maybe they convince him that there is a greater threat that only they can help him face. Along the way, Naruto might start to learn more about their motives and the secrets of their pasts. He could also be in a position where he has to use his own skills and values to influence them.
One possible plotline could be that Naruto has his own mission or purpose that is in conflict with Rias's plans or the world she is a part of. So, he decides to leave to pursue his own goals. For example, he might need to go back to the Hidden Leaf to protect it from a new threat that only he can handle. Another could be that Naruto discovers some dark secret about Rias or her group and can't stay with them any longer. He values his own moral code too much to be associated with something he deems wrong.
One possible plotline could be that Kushina's survival changes Naruto's upbringing completely. Instead of being an orphan, he grows up with a loving mother. This could lead to him being more confident and less of an outcast in the village at a young age. He might also learn about the Uzumaki clan's secrets earlier from his mother, which could make him a more formidable ninja even faster.
One possible plotline could be Naruto growing up with a sense of deep abandonment and having to face the world alone. This could lead to him having a much more cynical view of life. He might struggle more with controlling the Kyuubi's power as he has no guidance from Kushina. Another aspect could be his relationships with other characters like Iruka or Sasuke being different. Without Kushina's love, he may be more desperate for any form of connection.
One possible reason could be for Naruto's safety. Maybe she has to go on a dangerous mission and believes Konoha is the safest place for him. Another reason might be that she is forced by some powerful enemies who threaten Naruto's life if she doesn't leave him in Konoha.