It could be some water - dwelling dark creatures. Maybe mermaids with a malicious streak or some sort of lake - bound demons that were awakened when Hermione got too close. They might see her as an intruder and want to harm her, which is why Harry has to save her.
In this fanfiction, it could start with Hermione going to the lake for some research purpose. But things go wrong when she accidentally disturbs an ancient magic in the lake. Harry, who has a special connection to the magic around Hogwarts, senses her distress. He races to the lake and dives in. As he swims towards Hermione, he has to battle his own fears as well as the unknown threats in the water. Once he saves her, they realize that there is more to the mystery of the lake than they initially thought, and they team up to figure it out.
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.
Well, in many such fanfictions, Harry might use his magic skills. He could cast a powerful stupefy spell on the troll to stop it in its tracks and then quickly lead Hermione to safety. Maybe he also uses his quick thinking and knowledge of the Hogwarts corridors to find a hiding place where the troll can't reach them.
After Harry saves Hermione, their relationship could evolve in a more complex way. There could be a newfound respect between them. Harry might have a sense of pride in being able to protect her, and Hermione may feel a bit more vulnerable around him. This could lead to some awkwardness at first, but as they work through it, they become closer. They might start spending more time together, not just for school or magic - related things, but also just to be in each other's company. Their friendship could become the cornerstone of their lives, with Harry always being there to protect Hermione and Hermione always being there to support Harry with her knowledge and wisdom.
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.
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.
Maybe Viktor has been cursed in some way in the fanfiction, and his actions towards Hermione are involuntary. Harry, being observant, picks up on the strange behavior. He may call upon his friends for help, like Ron. Together, they could form a plan. Harry might use his invisibility cloak to get close to Viktor and Hermione without being noticed and then use a powerful stupefy spell to stop Viktor before he can harm Hermione. And then they would figure out how to break the curse on Viktor.
They could become friends. Draco, having been saved by Harry, might feel indebted to him. He could start to join Harry and his friends in some activities, slowly integrating into their group. Harry, in turn, would welcome Draco as he always believed in giving people second chances. They could then support each other in their studies and adventures at Hogwarts.
One possible plotline could be that Harry uses a powerful spell he's been secretly practicing to stun Bellatrix just in time as she's about to harm Hermione. For example, he might use a modified version of the Stupefy spell that's more powerful. Another could be that Harry manages to create a diversion, like summoning a horde of magical creatures, which distracts Bellatrix long enough for him to rescue Hermione.