Perhaps Naruto lies to Kushina about something major. Let's say he gets into trouble at school and instead of being honest, he tries to cover it up. When the truth comes out, Kushina could be so disappointed that she cries. Or if Naruto decides to leave the village without telling her first, knowing how much Kushina loves him and wants him to be safe at home. This sudden departure could break her heart and make her cry.
One possible scenario could be that Kushina's spirit somehow manifests and guides Naruto in a difficult battle. She might use her chakra to give him an extra boost or share some long - forgotten family jutsu with him. Another scenario could be that in a time - travel fanfic, Kushina actually gets to be there in person to save Naruto from a dangerous situation in his childhood that he originally faced alone, like the time he was ostracized in the village as a child.
Perhaps in the fanfiction, Kushina lied about Naruto's potential. She could have downplayed his abilities to keep him from being targeted too early. Like, if Naruto showed signs of having a powerful chakra reserve or a unique kekkei genkai, she might have lied to the village elders or other shinobi about it so that Naruto could grow up without too much interference or jealousy from others.
Well, one scenario could be that Kushina finds a fanfiction where Naruto has turned evil due to some dark force. Another might be that she discovers a story where Naruto is in a relationship that is completely out of character for him. Maybe she stumbles upon a fanfiction where Naruto has some really strange and overpowered abilities that don't fit the original Naruto universe.
Well, perhaps Katara blames Zuko for something that went wrong in their attempts to bring peace to the world. She might think he made a decision that cost them dearly. Her disappointment and anger could be so intense that she lashes out at him verbally. Zuko, who has been trying hard to redeem himself, is deeply hurt by her accusations and starts to cry. It could also be that Katara misunderstands Zuko's intentions in a situation. Say he was trying to protect her but it looked like he was being controlling, and when she confronts him about it, he can't handle the thought of her seeing him in such a negative light and cries.
One scenario could be that Naruto discovers some hidden secrets about Minato and Kushina that he interprets as them being selfish. For instance, he might find out that they had a choice to be with him but chose something else instead, which makes him angry and full of hatred towards them.
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 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.
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.