The plot could center around the mystery of Vault 99. When Harry finds out Malfoy has access to it, he starts investigating. He might discover that the vault holds some sort of power or knowledge that could change the wizarding world. Harry would then be in a battle of wits with Malfoy to either gain control of the vault's contents or prevent Malfoy from misusing them. This could involve sneaking around Hogwarts, using magic to uncover clues, and facing off against Malfoy's allies.
Hermione would probably be involved. She's always by Harry's side when it comes to solving mysteries. She could use her vast knowledge to help Harry figure out what's so special about Vault 99. Ron might also be there. He's Harry's loyal friend and would be ready to back him up in any adventure related to Malfoy and the vault.
In the fanfic 'Malfoy's Revelation', Malfoy is paired with Harry for a project. As they spend time together, Malfoy notices some strange behaviors from Harry, like flinching at sudden movements. After some snooping around, he discovers that Harry has been abused. This new knowledge makes Malfoy more empathetic towards Harry and he tries to help him in his own way, which includes standing up for Harry against some of their mutual enemies at Hogwarts.
One consequence could be that Hermione has to face the Malfoy family. They might try to bring her into their way of life, which she has always opposed. It would be a struggle for her to keep her own values intact while dealing with their pure - blood traditions.
One possible plot could be that Harry discovers he has some long - lost connection to the Malfoy family. Maybe he finds out through some ancient magic or a hidden family secret. This could lead to him having to re - evaluate his entire view of the Malfoys, especially Draco. He might start to understand Draco's actions in a different light and even feel a sense of kinship with him.
In some fanfictions, Hermione might find out she is a Malfoy due to a spell gone wrong. For example, a spell that was meant to reveal family lineages got mixed up and suddenly she has a connection to the Malfoy family in the magical world created by the fanfiction writer. It could also be a result of a hidden prophecy that links her to the Malfoys in an unexpected way.
Hermione would probably be very skeptical at first. She would want to research every aspect of this new discovery. Ron would be more likely to be angry or at least very confused. He has always seen the Malfoys as the enemy, so the idea of Harry being one of them would be hard to swallow. Draco, on the other hand, would be quite smug. He might think that Harry is finally realizing that the Malfoys are superior in some way.
Well, in this fanfiction, Percy might discover all sorts of treasures in the vault. Maybe it's filled with ancient magical artifacts that could give him new powers or abilities. It could also be a place full of secrets about his past or the world he lives in.
In this fan fiction, Harry might initially deny the whole thing. But as he starts to explore this new side of himself, he could discover some hidden secrets about the Malfoy family. This could change his perception of the Malfoys completely. And who knows, it might even lead to a new form of magic or power that he has access to because of his newfound 'Malfoy - ness'.
At first, Harry would probably be in shock. He's been through so much in his life, and this would be a huge new development. He might be a bit hesitant and scared, not sure if he's ready to be a father. But as time goes on, his Gryffindor courage would kick in and he'd start to take on the role with determination.