One possible reason could be for stealth. By using a female henge, Naruto might be trying to blend into a group where females are less likely to be suspected. For example, if he's infiltrating an enemy base that is more vigilant against male intruders.
One possible plot could be that Naruto accidentally uses a new type of henge that makes him disappear not just visually but also from the ninja world's chakra detection. His friends then go on a quest to find him. They might face various challenges and encounter old enemies who are taking advantage of Naruto's disappearance. In the end, they find a way to reverse the henge and bring Naruto back.
Well, it could be due to a disruption in the chakra control. If the character who performed the female henge loses focus or gets distracted, the chakra maintaining the transformation might falter and cause the henge to disappear. For example, if they are suddenly attacked or startled during the henge.
Another reason could be for disguise. Naruto might be in a situation where he needs to hide his identity. By covering his eyes, which are a very recognizable feature of his, he can make it more difficult for others to figure out who he is. This could be especially important if he is in enemy territory or trying to infiltrate a group secretly.
One reason could be to explore the darker side of the Naruto universe. Writers might want to see how the characters and the world would react to such a major loss.
One possible reason could be that a powerful dark magic spell has been cast on him. Maybe a new dark wizard or witch, created specifically for the fanfiction, has found a way to make him vanish to cause chaos in the wizarding world. Another reason might be that Harry has chosen to disappear himself. Tired of the constant attention and danger, he decides to go into hiding, perhaps using some long - forgotten magic or a powerful magical object to conceal his presence.
One possible reason could be a sign of extreme loyalty and friendship. Naruto might see Yang in a dire situation where she needs his arm for some crucial purpose, like to complete a powerful jutsu or to defend against an overwhelming enemy. He is known for his selfless nature, so sacrificing his arm would be in line with his character.
One possible reason could be for Naruto's protection. His father might think that by locking him away, he can keep Naruto safe from the many threats in the Naruto world, like powerful enemies who might target Naruto for his special powers.
Power imbalance could also be a reason. If Naruto's power suddenly goes out of control or he misjudges the Teen Titans' power levels and thinks they are a danger to his world or friends, he might take extreme actions. For example, if there's some kind of power - up in Naruto that makes him overly confident or paranoid, he could lash out at the Teen Titans thinking he's protecting something important.
One possible reason could be that the council has been secretly plotting against Naruto all along, perhaps trying to undermine his power or even get him exiled. Naruto might have discovered their malicious plans and decided to take pre - emptive action to protect himself and his friends.
One possible reason could be that Kushina was forced to leave Naruto due to some external threat she thought would endanger him more if she stayed. For example, if there were powerful enemies after her and she feared they would use Naruto to get to her.