The story could take a dark turn for Stiles. Without Scott, he might become more vulnerable and attract the wrong kind of attention. He could end up in a dangerous situation that forces him to grow and become stronger on his own.
Often, there's an immediate moment of shock. Then Scott might rush to Stiles' aid. Stiles could initially push Scott away, but then Scott would be persistent in trying to help. The story might then focus on Stiles' recovery, both physically and emotionally, with Scott by his side trying to make amends.
One possible reason could be a fundamental disagreement in their goals. Maybe Scott has a new mission that he believes Stiles would be a hindrance to, or perhaps their values have diverged. For example, if Scott becomes more involved with a new group that has a different ideology, he might feel the need to leave Stiles behind to pursue that new path.
Well, the story could develop in many ways. Ash might go into a deep depression at first. He has been with Pikachu for so long that its absence would be a huge blow. He could start doubting his abilities as a Pokémon trainer.
Well, it could go in many directions. For example, his family might start to search for him, which could lead to a series of adventures where they encounter new characters and face various challenges. His wife, if he has one in the story, might become stronger and more independent in his absence, vowing to bring him back.
At first, it might be a tentative alliance. Stiles could be initially drawn to Peter for his knowledge. Peter, seeing Stiles' potential, starts to include him more in his plans. As time goes on, they might develop a mutual understanding. Stiles begins to trust Peter more and more, and Peter starts to value Stiles not just for his help but also as a friend or something more.
It becomes strained. Trust is broken, and Stiles may start to distance himself from Scott. He might not believe in Scott's words or actions anymore, and there will be a lot of tension between them.
The story may develop in a way that Harry starts to suspect foul play. He could begin an investigation, enlisting the help of his friends. As for the kids, they could become more independent and resourceful. They might also form a stronger bond with Harry. And in some fanfictions, Ginny's absence could be a catalyst for a new and dangerous threat to emerge, which Harry and the kids have to face together.
In other cases, Harry might create his own new world, a sort of hybrid between the wizarding and Muggle worlds. He could gather other outcasts from the wizarding world who also want a different way of life, and together they build a community where they can use magic freely but also incorporate Muggle values and ideas. This new community becomes a haven for those who are tired of the traditional wizarding world's ways.
The story could develop in many ways. One way is that Naruto might become a target of the Akatsuki. Since he knows their secrets and has left their group, they would see him as a threat. This could lead to a series of battles where Naruto has to fight against the Akatsuki members one by one to protect himself and his village.
Stiles might initially be shocked. He has been a part of the pack for a long time, and Scott kicking him out would be completely unexpected. He could stand there in disbelief, unable to process what has just happened.