Well, in such a fanfiction, Harry might disappear to train in some hidden place, away from the prying eyes at Hogwarts. Maybe he goes to a secret location with a powerful wizard who teaches him advanced magic that he couldn't learn at school. This could include dark magic defenses or ancient spells.
It could be Dumbledore. Even if he's dead in the original story, in fanfiction, anything is possible. He might have left behind some kind of magic that allows him to train Harry from beyond the grave, or he could have faked his death to take Harry to a secret location for training.
In fanfiction, if Harry Potter disappears, it could lead to chaos at Hogwarts. His friends like Hermione and Ron would likely be on a desperate search for him. They might suspect the Dark forces at work again, and start investigating all the possible places where Harry could have been taken or hidden.
One possibility in this fanfiction is that Naruto's training with the Kyuubi helps him to better understand the nature of chakra itself. He could discover new ways to combine his own chakra with that of the Kyuubi, creating a unique and extremely powerful form of energy. This new form of chakra could give him an edge in future battles against powerful enemies. Also, his time training might be filled with various challenges and trials set by the Kyuubi, which would test his resolve and determination, making him an even stronger ninja in the end.
The setting in which Harry disappears and returns also matters. If it's in the middle of Hogwarts, the school would be in chaos. Teachers would be trying to keep the students calm while secretly searching for Harry. And when he returns, the reactions of different houses - Gryffindor being relieved and proud, Slytherin perhaps being suspicious - could add more layers to the story.
One idea could be a crossover where Train Heartnet, with his unique skills as a sweeper, somehow ends up in the wizarding world of Harry Potter. Maybe he's on a mission to retrieve a magical artifact that has fallen into the wrong hands in Hogwarts. His combat abilities and sharp senses would make for an interesting dynamic in the magical setting.
Merlin might start by teaching Harry the basics of magic from a different perspective. Maybe he would show Harry how to draw magic from the very essence of nature. For example, instead of using a wand in the traditional way, he could teach Harry to use his hands and the energy around him.
Anubis could train Harry Potter through a series of trials. These trials would test Harry's courage, wisdom, and his ability to face the unknown. For instance, he might be put in situations where he has to make difficult choices regarding life and death. Anubis would also likely teach Harry about the balance between light and dark magic. He would show Harry that there is power in the darker aspects of magic if it is used for the right reasons. This would be a completely new concept for Harry, as Hogwarts mainly focuses on the light side of magic. Through these teachings and trials, Harry would grow into a more powerful and well - rounded wizard.
Perhaps Harry is kidnapped by a mysterious and powerful magical being. This being has the ability to make Harry disappear without a trace. His friends then embark on a dangerous quest to find him, facing many magical challenges along the way. They might have to search in hidden and dangerous parts of the wizarding world that they have never been to before.
There could be. Fanfic writers often come up with unique concepts. The founders' trains might be used to transport students in a time long before the Hogwarts Express we know. It could be a way to show a different side of the founders' era, with different magical technologies or traditions associated with these trains.