One idea could be that Harry is under a dark spell that makes him kidnap Muggles, but then his friends try to break the spell and save him and the Muggles. Another could be that it's a case of mistaken identity and Harry is wrongly accused of kidnapping Muggles when he was actually trying to protect them from a real threat. Maybe in the fanfiction, Harry kidnaps Muggles to show the wizarding world how wrongly Muggles are treated by some wizards.
In this fanfiction, it could start with Harry having a strange dream that compels him to kidnap Muggles. As he does it, he realizes that there's a hidden message in this act. It turns out that there's a secret group of wizards who are using Muggles in a dangerous experiment. Harry kidnaps the Muggles to protect them from this group. He then has to figure out how to expose this group and return the Muggles to their normal lives without getting caught by the Ministry of Magic, which would surely misunderstand his actions.
Well, perhaps in this 'harry kidnap muggles fanfiction', Harry is being controlled by an ancient artifact. The artifact forces him to kidnap Muggles as part of a dark ritual. His Gryffindor courage still shows through, and he tries to resist as much as he can while his friends scramble to find a way to destroy the artifact. Or it could be that a new dark wizard has framed Harry for kidnapping Muggles to turn the wizarding world against him, and Harry has to clear his name while also ensuring the safety of the kidnapped Muggles.
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.
One idea could be muggles discovering a powerful magical artifact and trying to use it against wizards. Another could be wizards trying to hide their world from muggles who have become overly curious due to some strange magical events leaking into the muggle world. A third plot idea might be a group of muggles and wizards teaming up against a common enemy that threatens both their worlds.
One idea could be that Scabior kidnaps Hermione to use her knowledge for some dark wizard's plan. Maybe he's been promised a great reward. Another could be that he mistakes her for someone else at first but then realizes her true value.
Some muggles in fanfiction could be the relatives of a half - blood wizard. These muggles might have a hard time understanding their wizarding family member's abilities at first. They could be initially skeptical or even scared when they witness magic. However, as the story progresses, they might come to accept and even be in awe of the wizarding world.
Another concept could be a magical or supernatural 'kidnap love fanfiction'. The kidnapper could be a supernatural being, like a vampire or a werewolf. He kidnaps the human he loves because he wants to protect them from other dangerous supernatural creatures. But the human doesn't understand his motives at first and struggles against him. As time passes, they develop a strange and intense love relationship.
One alternative could be a story about the Dragonborn going on a quest to discover their true heritage. They could travel across different lands, meet various characters who help or hinder them in their search for knowledge about their family and their unique powers.
Some fanfictions might have a plot where the muggle family tries to 'cure' Harry of his magic. They could take him to various doctors or therapists thinking he has some sort of mental disorder. Meanwhile, Harry is feeling more and more isolated and confused. When he does meet someone from the wizarding world, like a Hogwarts teacher who comes to check on him, it's a moment of great relief and the start of a new journey.
Perhaps a story where Harry helps a muggle child who is being bullied. He uses his magic to give the child the confidence to stand up for himself. He might also use some minor spells to make the bully realize the error of their ways, but in a way that doesn't expose the wizarding world to the muggles.
One interesting concept could be how muggles react to the magical world. For example, they might be in awe of the simplest spells like Lumos. Another could be the friendships that form between muggles and wizards in the fanfiction. It can show a unique dynamic as they learn from each other.
One plot idea could be that Draco and Blaise kidnap Hermione as part of a misguided attempt to gain some sort of leverage in the wizarding war. Maybe they think they can use her knowledge to find a way to end the conflict on their terms. Another could be that they believe she has a hidden power or secret that they want to uncover for their own gain. For example, they might think she has a connection to a powerful magical artifact that they are desperate to get their hands on.