It could be a new dark wizard who has been secretly plotting in the shadows. This wizard might be jealous of Harry's fame and power, and decides to make him disappear so that he can rise to power unopposed. He could have a group of followers who are experts in dark magic and are able to carry out his plan to make Harry vanish.
Maybe the main villain is a powerful magical creature that has a grudge against humans in general and Harry in particular. For example, a basilisk that has somehow escaped death again and has developed the ability to make people disappear. It could be lurking in the sewers or an old abandoned part of Hogwarts, waiting for the perfect moment to strike and make Harry disappear.
In some fanfictions, the main villain could be an alternate version of Voldemort. This version might be from a parallel universe where he was more powerful and managed to make Harry disappear before he could become a threat. This alternate Voldemort could then start to invade Harry's world, and the remaining characters have to figure out how to stop him and bring Harry back at the same time.
A secret society that has been observing the Avatar from the shadows could be the main villain. They believe that Aang's power is too great and unpredictable, so they use some ancient and powerful artifacts to make him disappear. The heroes would then have to figure out how this society operates and find a way to reverse the spell or device that made Aang vanish.
Orochimaru could be a likely main villain. He has always been interested in Naruto's power and body. Maybe he finally devises a plan to kidnap Naruto and use his body for his own reincarnation experiments.
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.
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.
Perhaps a powerful magical being from a different realm is the antagonist. This being might mistake Hermione for someone else or see her as a key to something in the wizarding world. So, it uses its magic to make her disappear. This being would be very difficult to defeat or negotiate with, making it a huge challenge for those trying to find Hermione.
The Queen of Hearts would make a great main villain. Her tyrannical rule and quick temper in the original Wonderland story could be amplified in a fanfiction. She could be a powerful dark magic user who sees Harry as a threat to her rule and tries to stop him from achieving his goals in Wonderland.
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.
It could be Salem. She has always been interested in the power of the silver eyes, and Ruby having those eyes makes her a prime target. Salem might send her minions to kidnap Ruby, which would lead to her disappearance.
Voldemort could still be the main villain. He might target Harry as usual, but this time the Weasley twins get involved more directly. They could use their cleverness and inventions to try and thwart Voldemort's plans, like creating anti - Dark Arts devices that can detect Death Eaters.
Maybe Voldemort's old followers who are still up to no good. They might think that by getting Harry to kidnap Muggles, they can bring back the dark days under Voldemort's rule. They could be using some sort of dark magic to influence Harry's actions.