Harry dies trying to reach Sirius when he falls through the veil during the Battle of the DoM. Remus is able to stop Hermione from rushing in after him at the last second, however. She grieves at first, stuck in a near unresponsive depression on the outside but battling her morals with her hatred for those who want to kill him. She soon peruses a path that leads her to an ancient, powerful magic; the only catch is the consuming parasite that lives within it. She slowly gains magical abilities ascending above that of the world's most powerful wizards and witches, but the parasite warps her mind into something darker and she soon targets anyone who tried to manipulate or hurt Harry in the slightest, then the people who wronged him and her even if it was only once, before she slowly becomes consumed by the dark parasite.
Harry wakes up a little less than five years after Hermione rose to power. His parents are there and tell him that he needs to go back and save everyone from a different tyrant. He's thrown back into the real world again, but everything is different. He's older now, of course, but that's hardly what catches his attention. Muggles are boarded in their homes, hiding behind walls and woods of planks while the Wizarding World is practically enslaved. Harry finds his friends again, but they're servants simply trying to get through the day without trouble.
When he finds Hermione, she's nothing like herself. Her eyes are black and unsettling. She's mad, almost like Bellatrix, but in a smart kind of way that makes his head spin. The parasite has consumed her so much that only the tiniest bit of the old Hermione he knew shows through, but that's all he needs. He risks his life to bring back his best friend and the girl he admits that he has always loved.