It could also be a result of a magical bargain or curse gone wrong for the Malfoys. Suppose there was a powerful dark magic object in the manor that got out of control. Hermione, with her vast knowledge of magic, manages to contain it. In the process, she ends up being the rightful owner according to some ancient magic laws. This would make for an interesting plot twist in the fanfiction.
Well, one scenario could be that they are attending a peace - making event. Hermione, being the diplomat, tries to make amends between the Weasleys and the Malfoys, and Ron is there just to support her and make sure she doesn't get into any trouble. But things quickly go awry as old rivalries resurface.
Perhaps they are there to rescue someone. Hermione might come up with a clever plan involving potions and charms to get past the manor's defenses. Ron, with his loyalty and determination, would be right by her side, ready to take on any danger that comes their way.
In some fanfictions, Ron and Hermione could be at Malfoy Manor for a diplomatic mission of sorts. The wizarding world is in chaos, and they are sent to try and convince the Malfoys to switch sides. This would be a very difficult task as the Malfoys have long been associated with the dark side. But Ron's loyalty and Hermione's persuasion skills could potentially make a difference.
One storyline could be Hermione using the manor as a place to gather and protect magical creatures. Since she is known for her love of all living things in the wizarding world, she could transform the manor's grounds into a sanctuary. The Malfoy family's old dungeons could be converted into a healing area for injured creatures. This would bring a new sense of purpose to the once - dark and foreboding manor.
One possible scenario could be that Draco has a change of heart at Malfoy Manor. He might secretly try to protect Hermione from the other Death Eaters. Maybe he uses his knowledge of the manor's secrets to hide her or mislead the others. For example, he could tell them she escaped through a certain passage when in fact he has her hidden in a secret room.
A common plot is that they are sneaking into the manor to steal something important, like a magical artifact. Ron would be on the lookout for any danger while Hermione figures out how to bypass the manor's defenses.
It could be that in the manor, they discover they have more in common than they thought. Both are under a great deal of pressure - Draco to please his family and uphold the Malfoy name, and Hermione to fight against the Dark forces. As they interact more, they begin to understand each other's struggles, and this understanding leads to a deeper connection. Maybe they start to communicate without words, just by looks, as they plan their next move to survive or escape the manor.
Ron could become more confident in his relationship with Hermione. After seeing her in such a dangerous situation at Malfoy Manor, he realizes how much she means to him and is more assertive about his feelings. He might also grow in his magical abilities as he wants to be better able to protect her.
There are several motives. Firstly, to add a sense of tragedy. The 'Harry Potter' series has its share of losses, but Hermione's death in a fanfic at Malfoy Manor would be a new level of tragedy. It could also be to rewrite the story in a more 'grimdark' style. This would attract readers who are interested in seeing a different side of the wizarding world. Moreover, it might be an attempt to explore the consequences of a major character's death on the overall plot. For example, how would the fight against Voldemort be different without Hermione's intelligence and magic skills?