Perhaps in the fanfiction, Kushina takes advantage of Naruto's connection to her by influencing his decisions in a way that benefits the village in the long run. For example, she might guide him towards making alliances or taking on certain missions that are crucial for the safety and prosperity of Konoha. This could involve her using her memories or her spirit's influence over Naruto to push him in the right direction.
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.
Kushina could develop in terms of her relationship with Naruto. At first, if she is just taking advantage, it might be a one - sided relationship. But as the story progresses, she could grow to truly care for Naruto as a mother figure. This could be shown through her sacrificing her own interests to protect Naruto or by being more empathetic towards his struggles.
Well, one possibility could be that Kushina takes Naruto away to protect him from the dangerous world of shinobi. Maybe she wants to raise him in a peaceful place away from the constant threats and battles in the Hidden Leaf Village.
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.
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.
Naruto might discover new Uzumaki techniques. Since the Uzumaki clan was known for their strong sealing jutsu, he could learn some advanced sealing techniques during his visit to Whirlpool. Maybe he'd find a special scroll left by his ancestors that contains a powerful jutsu.
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.
Maybe she's been possessed. In some fanfictions, characters can be taken over by dark forces. So Kushina could be under the control of some evil entity and that's why she hurts Naruto.
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.