It could be that they are kidnapped by a dark wizard who has found a way to make them vanish without a trace. They are held in a hidden lair, and during their captivity, they manage to form an alliance with some of the wizard's captives and together they plan an escape.
One possible plot could be that they disappear to a parallel magical dimension. In this dimension, they have to learn new forms of magic to survive and find their way back home. Maybe they encounter strange magical creatures that are unknown in their own world.
Perhaps they disappear because of a powerful spell gone wrong. They end up in a time - locked area within Hogwarts that was sealed off long ago. There, they discover secrets about the founders of Hogwarts and have to use this knowledge to break free and reappear in their own time.
Well, in some 'Hermione Disappears' fanfiction, it might be that she is targeted by a group of anti - Muggleborn wizards. They manage to make her vanish using some dark magic. Her friends, Harry and Ron, then start a frantic search. They might follow a series of mysterious clues she left behind before disappearing. It could also be that a time - traveling mishap causes her to disappear from the current timeline and she is stuck in another era.
It could be that Naruto sacrifices himself to seal away a great evil. However, his friends don't believe he's truly gone and embark on a journey filled with self - discovery and growth as they try to find a way to bring him back. Along the way, they might encounter other lost souls or forgotten powers that could potentially help in their quest.
Well, it's a rather dark concept. One possible plot could be that in a dark, alternate universe, Harry is under some sort of dark magic influence which makes him act against Hermione's will. But this is very much against the essence of their characters in the original series.
In some fanfictions, it could be a misunderstanding that spirals out of control. Hermione and Ron misinterpret one of Harry's actions. For instance, Harry might be trying to protect them in a secret way, but it looks like he's up to something bad. Their lack of trust then grows, and they end up betraying Harry, perhaps by not coming to his aid when he really needs them, which could have serious consequences for Harry.
Perhaps in this fanfiction, it's part of a bet or a challenge. Harry loses a bet to Hermione and has to be her slave for a certain period. This could lead to various comical situations as Harry tries to fulfill Hermione's often demanding tasks.
One possible plot could be that Ron and Hermione suspect Harry is involved in some dangerous secret magic that could put him in harm's way. So they spy on him to find out more and end up discovering it's all a big misunderstanding. Maybe Harry was just trying to surprise them with a new spell he learned.
One possibility could be that Harry is so traumatized by the war that he wants to isolate himself from the wizarding world. He might go into hiding in a remote, Muggle - free location to deal with his inner demons.
Voldemort could be the antagonist. Even if he was defeated in the original story, there could be a scenario where some remnant of his dark magic causes Harry and Hermione to disappear. Maybe he had a secret plan that was set to activate after his death and it involved taking them out of the picture.
One possible plot could be the secrecy and the struggle to keep it hidden from their friends. Another might be the way they deal with the reactions of Ron and other close friends. It could also involve how they plan for the future with a baby on the way in a world full of magic and danger.
One plot could be that Draco disappears because he's on a secret mission for the Order of the Phoenix. He has to go undercover in the Death Eater ranks and cut off all contact with his friends at Hogwarts to keep them safe. Another idea is that he disappears due to a family curse that suddenly activates, and he has to find a way to break it while being in a hidden magical realm. A third plot could be that Draco fakes his disappearance to start a new life away from the expectations and pressures of the wizarding world.