The story could end with a realization of their mistake. Once they understand that they were misled or misinformed, they could try to reverse the damage. Maybe they use some kind of time - travel or magic to fix what they've done and ensure Minato grows up as he should in the original Naruto story.
One possible fanfiction could be about Kagome somehow traveling to the Naruto universe. Maybe she meets Minato and they form an alliance. And she discovers that Naruto is Minato's son. Shippo could be a unique addition, perhaps he has some special abilities that are useful in the Naruto world.
One possible reason could be an alternate timeline gone wrong. Maybe some dark magic or a powerful villain has manipulated Kagome, Shippo and Naruto into thinking baby Minato is a threat to their world. Another reason could be a misunderstanding. For example, they might believe that Minato is somehow related to a future danger and they are trying to prevent it before it starts. However, this is a very dark and unorthodox scenario considering Minato is a beloved character in the Naruto universe.
Kagome could be a foreign element that brings new magic or abilities. For instance, her spiritual powers could be used to combat certain dark forces in the Naruto world. Shippo, being a fox - demon, could have a connection with Naruto due to his own jinchuriki status. They could all bond over their unique powers and the fact that Naruto is Minato's son.
I'm sorry, but 'lemon' in fanfiction often implies inappropriate or adult - themed content. However, you can look for general Kagome and Shippo - centered fanfictions on platforms like FanFiction.net or Archive of Our Own without focusing on the 'lemon' aspect.
In fanfiction, it might be used to add a touch of warmth and domesticity. Reading fairy tales to Shippo could be Kagome's way of passing on knowledge or just having a relaxing time together. It can also help in character development for both of them, showing their softer sides.
One possible plot could be that their own group betrays them. Maybe for some powerful magical item or a secret that Kagome holds. Shippo, being young and not as powerful, is easily overpowered. Kagome, on the other hand, tries to fight back but realizes she's been tricked by those she trusted. She then has to find a way to escape with Shippo and seek revenge or justice.
It could be a jealous member of their group. Maybe someone who is envious of Kagome's special powers or the attention Shippo gets. This person might spread false rumors about them, leading to the rest of the group turning against them.
As Shippo grows up under Kagome's care, their relationship deepens. They go through many adventures together, facing demons and other challenges. Through these shared experiences, they build a strong bond. Shippo might start to see Kagome as a mother figure, and Kagome sees Shippo as her own family. They support each other emotionally, like when Shippo comforts Kagome after a tough battle, or Kagome encourages Shippo when he's doubting his abilities.
Well, often there's a theme of forbidden love, as their relationship might not be a typical or expected one in the original Inuyasha series. There could also be themes related to self - discovery for both characters. As they engage in this relationship, they might learn new things about themselves. And of course, the 'lemon' part usually involves some level of sexual tension and exploration, but this should be within the boundaries of appropriate fanfiction and not cross into inappropriate territory.