Maybe Pikachu is feeling neglected by its trainer. If the trainer has been paying more attention to other Pokemon or is too busy with something else, Pikachu might decide to run away to get some attention.
Perhaps Pikachu has gotten into an argument with its trainer. Maybe the trainer made a decision that Pikachu didn't like, such as trying to make it evolve when Pikachu doesn't want to. This could lead to Pikachu running away in a fit of anger or disappointment.
It could be that Pikachu has sensed some danger in the area. For example, if there is a powerful and menacing Pokemon nearby that Pikachu thinks it can't face with its trainer, it might run away to protect itself and its trainer. In fanfiction, the author might create a situation where Pikachu has a premonition of some sort of impending doom and chooses to flee.
One possible reason could be that Pikachu is separated from Ash. In many fanfictions, their bond is so strong that being apart would be extremely distressing for Pikachu, leading it to cry.
One common reason could be jealousy among other Pokemon. Some Pokemon might be jealous of Pikachu's closeness to Ash and its popularity. So, they might plot against it and end up killing it. Another reason could be a misunderstanding. For instance, a wild Pokemon might misinterpret Pikachu's actions as a threat and attack it fatally.
Perhaps Naruto discovers something about Itachi that the rest of the world doesn't know and he needs to run away to protect that secret. It could be a powerful jutsu or a message that could change the balance of power in the ninja world.
Another reason could be that she wants to explore the world on her own terms. In the fanfiction, Mirabel may be tired of always being in the family's protective bubble. She desires to see what lies beyond the village and the mountains, so she runs away to start her own adventure.
In the 'run away children story', sometimes children run away because of a lack of understanding or communication at home. Parents might be too strict or not pay enough attention to their children's feelings. The children then think running away is the only way to get noticed. Also, problems at school like bullying can lead to children running away. They may feel that they can't face the bully anymore and choose to leave.
A common reason could be a desire for adventure. Legolas, being an elf, might feel the need to break free from the monotony of his daily life. So he runs away to explore new lands and have exciting experiences.
One possible reason could be that he feels misunderstood by his family or friends. Maybe he has some secrets that he's afraid to share, and the fear of being judged makes him run away.
In some fanfictions, it could be that he has made a big mistake. For example, if his actions as Spider - Man led to the harm of an innocent person. He would be so guilt - ridden that he decides to run away from everything, including his friends and family in Queens.
She could run away because of a broken heart. Maybe she had a relationship that ended badly, and she needs to get away from the memories. In the process of running away, she could meet new people who help her heal and grow as a person. This type of storyline often explores the more vulnerable side of fem Tsuna.
In fanfictions, Naruto could run away from his family due to emotional abuse. If his family members constantly put him down, criticize his abilities, or make him feel unworthy, he'd likely want to escape. Also, if his family is involved in some political intrigue that he doesn't want to be dragged into. For instance, they might be making deals with other clans that Naruto disagrees with. Additionally, if there is a new family member introduced, like a step - sibling who is favored over him and he feels unloved, that could prompt him to run away.