One possible plotline could be that they fall in love gradually. Maybe they start as friends who bond over shared interests or experiences in the wizarding world. As their relationship deepens, they decide to keep it a secret to avoid unwanted attention or interference. Another aspect could be how they deal with their families. Harry has his own complex family history and Daphne might have expectations from her family. They would need to navigate these challenges while keeping their marriage under wraps.
In another scenario, Daphne could be in some sort of trouble, and Harry, being the hero he is, decides to help her. It could be related to her family's dark past catching up with her or a dangerous magical artifact she has come across. As he helps her out of the situation, their bond deepens. Harry then has to decide whether his feelings for her are just a result of the rescue situation or something more profound.
One possible plotline could be them teaming up to solve a mystery within Hogwarts that the teachers are unable to figure out. Maybe it's about a hidden chamber or a strange magical occurrence. Another could be Daphne helping Harry deal with his PTSD from his encounters with Voldemort. They could also form a study group together and end up learning new and rare magics.
One possible plotline could be that it's a political arrangement. Maybe there's some sort of wizarding world politics where uniting the Potter and Greengrass families is seen as beneficial for stability. Harry might initially resist but then gradually find out that Daphne has her own charm and they start to develop a relationship based on mutual understanding. For example, they could bond over their shared experiences in the wizarding world, like dealing with pure - blood prejudices.
One possible plotline could be that they start to secretly help each other with their studies. For example, Draco might be struggling with a certain type of magic that Harry is good at, like Patronus Charms. In secret, Harry could give Draco some tips. Another could be that they team up to solve a mystery in Hogwarts that no one else is aware of. They might discover a hidden chamber or a secret spellbook together. They would have to keep their friendship a secret because of the rivalry between Gryffindor and Slytherin. Their friendship could also be tested when their respective houses are in competition, but they still find ways to support each other on the sly.
Yes, there are likely many fanfictions with such a plot. Fanfiction writers often come up with creative scenarios like this. You can search on popular fanfiction websites using relevant keywords to find them.
It could be that Daphne has a personal connection to Harry that she's not aware of until she starts investigating the strange magical disturbances around the Dursleys' place. Once she realizes it's Harry in trouble, she enlists the help of her friends or some sympathetic wizards to break Harry free. She might also face some challenges along the way, like dealing with the Dursleys' resistance or the Ministry of Magic's rules about interfering in Muggle affairs.
Well, perhaps they meet in a secret corner of Hogwarts, like in the Forbidden Forest during a full moon. They start sharing their secrets and realize they have a special connection that they have to keep hidden from their friends and families because of the different houses they belong to and the expectations that come with it.
One possible plotline could be that Harry discovers a hidden family connection to the Death Eaters. Maybe his real parents were involved in some dark magic and he starts to explore this side of his heritage, which gradually makes him more sympathetic to the Death Eaters. Another could be that he is tricked by a powerful dark wizard into believing that the Death Eaters' goals are actually good for the wizarding world, so he starts working with them secretly.
Perhaps Harry and Daphne are part of a secret organization in the fanfiction. Daphne betrays Harry by revealing his identity to the enemy for some personal gain, like protecting her family from a threat the enemy made. Then Harry has to deal with the consequences of her betrayal and also figure out if he can forgive her.
One plotline could be that they secretly married to protect Ginny from a dark wizard who has a vendetta against Harry. By being secretly married, they think they can keep Ginny out of harm's way. Another could be that they did it on a whim during a romantic getaway and then decide to keep it a secret just for a while to enjoy their private time together.