One possible reason could be a powerful enemy capturing them. In the Naruto world, there are many strong villains who would love to get their hands on an S - Class ninja for their power or knowledge. Another reason might be that they are on a top - secret mission that requires them to disappear for a while.
Well, sometimes in fanfic, the S - Class ninja might go missing because of a personal vendetta. Maybe they are being hunted by someone from their past and they have to go into hiding. It could also be that they are exploring a dangerous and unknown part of the Naruto world, like a hidden dimension, and get lost or trapped there.
One idea could be exploring the backstory of an S - class missing - nin. Maybe they had a noble reason to turn their back on the village at first, like trying to protect a loved one from a corrupt system within the village.
There's a fanfic series that focuses on an S - Class missing during a major war in the Naruto world. The story follows a young ninja who discovers clues about the missing S - Class and starts to unravel a conspiracy. This fanfic has great character development as the young ninja grows throughout the story while trying to find out what really happened to the S - Class shinobi.
Well, in a girl missing story, she might have been a victim of human trafficking. Some criminal gangs target young girls. Or it could be due to a natural disaster. Say, if there was an earthquake or a flood, she could have been separated from her family and be missing. Mental health problems can also be a cause. If she was suffering from depression or some other mental illness, she might have wandered off without realizing.
Possible reasons in the 'Missing at 17' real story include mental health issues. A 17 - year - old struggling with depression or anxiety might decide to disappear as a way to escape their internal turmoil. Also, it could be due to a relationship gone wrong. If they had a bad breakup or were in an abusive relationship, they might run away. Additionally, it could be related to educational stress. Failing grades or pressure to perform well in school could push them to leave.
Poison or some sort of harmful jutsu effect. Maybe an enemy uses a special poison or a jutsu that slowly weakens Naruto's body. In the fanfic, this could be a new and unique type of attack that he has not encountered before, and his body is not able to withstand it, resulting in fainting.
One possible reason could be that she's on a secret mission. Maybe Ozpin sent her on a dangerous errand without telling the others to protect them. For example, he might have discovered a new threat related to Salem and needed Ruby to gather intel quietly.
One reason could be to test Konoha's security. Naruto might want to see if there are any loopholes in the village's defenses. So, he sends his clones to infiltrate and find out.
One possible reason could be that he is influenced by Orochimaru's techniques. Maybe he discovers some of Orochimaru's old research and figures out how to use snake summoning for his own good. Another reason might be that he is trying to find a new power source to defeat a very powerful enemy that normal jutsu can't handle.
Perhaps in the fanfic, Hinata has fallen in love with someone else. It could be a new character introduced in the fanfic's universe or someone she has come to know better over time, leading her to reject Naruto.
In some fanfics, there could be a misunderstanding. Suppose Kushina did something that Naruto misinterpreted as harmful to him or his friends. This misinterpretation could lead to his hatred. For example, if Kushina was involved in a mission that Naruto thought put the village at risk, but in reality, she had no choice.