Perhaps there could be a magical virus in the wizarding world that causes people to lose their memories like in the Maze Runner. Harry and his friends have to work with the Maze Runner characters to find a cure before it's too late.
Another idea is that the Death Eaters in Harry Potter create a new kind of maze similar to the one in the Maze Runner as a form of torture or experiment. Harry and his friends then team up with the Gladers to escape this new, magical maze.
Hermione would probably try to study the Gladers and their society. She could compare it to the wizarding society she knows. Meanwhile, Minho from the Maze Runner would be eager to learn about the magic that could potentially help them in their fight against the Creators. They would exchange knowledge and skills, like the Gladers teaching the wizards how to run fast and be more physically fit, while the wizards teach the Gladers some basic spells for protection.
Well, perhaps a crossover where the Volturi from Twilight are intrigued by the experiment of the Maze Runner world. They might see it as a new form of control over a large group of humans. Meanwhile, Thomas from the Maze Runner could have some sort of special connection with a Twilight character, like Bella, and they work together to break free from both the Maze and the Volturi's potential threat.
One interesting crossover could be the characters from Maze Runner finding themselves in the wizarding world of Harry Potter. They might be amazed by the magic and spells, while the Hogwarts students could be intrigued by the Gladers' survival skills. For example, Thomas could befriend Harry and they could team up to solve a mystery that involves both the Maze and the Dark Arts.
The idea of a group working together against a common enemy, which is prominent in Maze Runner, can be added to Harry Potter fanfiction. The Hogwarts houses could form an alliance similar to the Gladers. They could fight against a new dark force that is trying to take over the wizarding world. Each house could bring their unique skills, just as the Gladers had different roles in the Maze.
In some fanfics, a plot twist could be that Voldemort teams up with the Creators from Maze Runner. This completely changes the power dynamics as the combined evil forces pose a huge threat to the protagonists. It makes for a very intense read as the heroes have to find new ways to fight back.
One great Harry Potter Maze Runner fanfiction is 'The Crossover Quest'. It combines the magical world of Harry Potter with the post - apocalyptic setting of Maze Runner in a really interesting way. The characters from both universes interact in unexpected ways, like Hermione using her intelligence to solve the maze puzzles.
One idea could be exploring the backstories of the characters more in - depth. For example, what was Thomas' life like before he entered the maze? Another idea is to create an alternate ending where the Gladers find a different way to escape the maze and deal with the outside world. You could also write a fanfiction about a new group of people who enter the maze after the events of the original story and how they interact with the remaining elements of the maze and any surviving Gladers.
One possible plot could be that the Gladers from Maze Runner find themselves in the Avengers' universe. Maybe they are mistaken for threats at first. The Avengers would be confused by their strange clothing and the fact that they seem to be a group of kids with survival skills. Then, they realize that the Gladers are also fighters against an oppressive force, just like them. They could team up to fight a common enemy that has somehow managed to cross between the two universes as well.
One idea could be exploring the backstory of the girl character before she entered the Maze. Maybe she had a special talent or a hidden past that no one in the Glade knew about. For example, she could have been a trained fighter in a secret society outside the Maze world.
A cool plot for the maze runner fanfiction could be that there is a traitor among the Gladers who is secretly working for the people who put them in the maze. This traitor could be slowly sabotaging their efforts to escape. Or perhaps the maze starts to change in really strange and unpredictable ways, like the walls start moving at random times instead of just at night. The Gladers then have to figure out a new strategy to deal with this. And what if there were other groups of kids in different mazes and they somehow find a way to communicate and team up to escape all the mazes together.