In this type of fanfiction, it could be that Kushina has a misunderstanding about Naruto's goals. For example, if Naruto starts to befriend some people from other villages that are seen as potential enemies by Konoha. Kushina, being a very loyal Konoha - nin, disowns him. Naruto would have to prove that his actions are for the greater good of all villages and not just Konoha.
In such a fanfiction, the plot might involve Naruto feeling extremely alone and betrayed. He could start to question his self - worth. Maybe he'll set out on a journey to prove himself not only to the clan but to the whole village. He might find new allies outside the clan who see his potential and help him grow stronger.
One possible plot could be that Kushina, using her unique abilities or knowledge, helps Naruto gain an edge in his training. Maybe she imparts some secret jutsu or gives him advice on how to better control his chakra, which he then uses to overcome a powerful enemy.
Maybe in the fanfiction, baby Naruto has a nightmare. Kushina then holds him close, reassuring him that he's safe. She could tell him stories about his father, Minato, and how they both love him very much. This would comfort Naruto and he'd soon fall back asleep in her warm embrace.
It could also be due to a prophecy. Suppose there's a prophecy that Naruto will bring great disaster in the future. His parents, believing in the prophecy, might decide to disown him in an attempt to avoid that future. They might think that by cutting ties with him, they can somehow change the course of events.
One possible plot could be that Lemon has some special knowledge or power that she passes on to Naruto, while Kushina looks on with pride. Maybe Lemon has a connection to an ancient ninja art that Naruto needs to master to defeat a new threat in the village.
Perhaps in this one - shot, there is a magical spell that temporarily brings Kushina's spirit back to the world of the living. Naruto meets her and they have a long conversation. Kushina shares her experiences and wisdom with Naruto, and Naruto tells her about all the things he has accomplished and how he has made their family proud. This encounter gives Naruto a new sense of purpose and connection to his family heritage.
One possible plot could be that Lemon, Naruto's sister, discovers some hidden jutsu that Kushina once knew. Naruto and Lemon then train together to master it. Along the way, they face challenges like other ninja clans trying to stop them as they fear the power of this new - found jutsu. And in the end, they use the jutsu to protect their village and honor Kushina's memory.
One possible reason could be some sort of dark influence or curse that makes her lose her maternal instincts. Maybe a powerful enemy targets her and in order to protect Naruto from further danger related to her, she feels forced to abandon him. Another reason might be that she is made to believe false information about Naruto, such as that he will bring great disaster to the village in the future.
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.
It could also be due to some external influence. Perhaps an enemy used some kind of mind - control or manipulation on Kushina. They made her think that Naruto was a threat, so she decided to disown him. In the Naruto universe, there are many powerful villains who could potentially do this kind of thing.