The plot could involve Hermione being held captive by a dark wizard who wants to use her intelligence for evil purposes. Harry, using his invisibility cloak, infiltrates the wizard's lair. He battles the wizard and his minions using his wand and the spells he's learned. He manages to free Hermione and they escape together, with Harry using a portkey he had prepared in advance. Along the way, their friendship deepens as they rely on each other for survival.
Well, it could start with Hermione showing signs of distress. Harry notices and starts to investigate. He finds out that there's a group of Slytherins who are using dark magic to mentally abuse Hermione, making her doubt her own abilities. Harry then challenges them to a wizard's duel and wins, forcing them to stop their abuse.
One possible scenario could be that in this fanfiction, Harry discovers that Hermione is being bullied by some dark - minded students at Hogwarts. He steps in immediately, using his skills and the respect he has among his peers to put an end to it. Maybe he threatens the bullies with exposure to the professors if they don't stop.
He could use his position of authority. Snape might confront the abuser directly. Since he's a teacher, he has the power to intimidate and put a stop to any immediate harm. He could also give Hermione a safe place to stay, like his own quarters (if it's within the rules of the fanfiction world).
Perhaps in the fanfiction, Cormac invites Hermione to a secret gathering, but his intentions are not so noble. Ron finds out and races to the location to save Hermione. This act of heroism by Ron might make Hermione question her feelings for him. She might start to see him as more than just a friend, especially if Ron shows a side of himself that she hasn't fully appreciated before. The story could then follow how their relationship evolves from this event.
In this fanfiction, it could be that Ron is under the control of a powerful wizard who wants to get to Hermione for some reason. Charlie discovers this plot and decides to protect Hermione. He sets up various traps and wards around the place where Hermione is staying. When Ron, being controlled, tries to attack Hermione, Charlie is there to intercept him, engaging in a magical duel if necessary to save Hermione.
A common plot element is the discovery of Hermione's situation. Usually, Remus somehow becomes aware that Hermione is in danger or being abused. It could be through his own observations, or maybe Hermione reaches out to him for help.
In some fanfictions, Hermione might use her intelligence and magic skills. For example, she could use a powerful spell to create a distraction at the Dursleys' place. Maybe a spell that makes all the dishes in the kitchen start flying around, causing chaos. Then, while the Dursleys are distracted, she could quickly grab Harry and apparate away to a safe place, like the Burrow or a hidden wizarding location she has prepared in advance.
In this fanfiction, perhaps Hermione uses her vast knowledge of magic. She might save the Weasleys from a dark wizard's attack. Maybe she discovers a powerful spell to counter a curse aimed at the Weasley family.
Well, it could be that Hermione uses her time - turning device to go back in time and warn the Potters about Voldemort's plan. Maybe she disguises herself and manages to get into their hiding place, then uses her magic skills to set up powerful protective spells around them that Voldemort can't break through.
Perhaps Draco saves Hermione in a very public and unexpected way. This could lead to a huge scandal in the wizarding world. Lucius might be shamed and lose a lot of his influence among the Death Eaters. Draco, on the other hand, might find himself an outcast among his own family and former friends. Hermione, feeling indebted to Draco, might try to protect him from the backlash, which could further develop their relationship in an interesting way. It could also be that Draco's act of saving Hermione is part of a prophecy that neither of them knew about. This could add a layer of mystery and destiny to their story.
One scenario could be that Draco witnesses Hermione being bullied by some Death Eater - sympathizing students. He steps in and uses his quick wit and knowledge of magic to outsmart them. Another could be in a situation where Hermione is being wrongly accused of a crime and is facing abuse in the form of unjust imprisonment. Draco, having some influence in the Ministry due to his family, intervenes and clears her name.