"The Peace of Death" by SymphonySamurai.
Harry is sentenced to death and thrown into Azkaban, after Unspeakables found Dumbledore's journals. They were going to put all the horcruxes through the Veil of Death, including Harry.
Lucius Malfoy breaks Harry out of Azkaban.
He goes to Grimauld Place and meets Ginny, Luna and Neville there. Lavender Brown is there too as is Mrs. Tonks.
Harry explains how he has escaped.
When Harry asks where Hermione is, Ginny tells him that Hermione was dropped off at St. Mungo a couple of months ago, was told she had a severe reaction to a potion, and died a few days later.
She goes further that there wasn't any lead as to who poisoned Hermione and the case got shelved at the Ministry according to Ron. Ginny also says that when Ron was told Hermione died, he took a few months off of training and was acting weird.
Harry asks then why it took so long before he was informed and when Ginny says that she was listed as next of kin, she starts explaining how that came to be.
Hermione took it to the next level to try and find a way to get Harry out of Azkaban. She practically moved into the Black Library. She wouldn't have been eating if they didn't bring anything to her. She only slept if she passed out from exhaustion.
Her relationship with Ron went from bad to worse and Ron wouldn't leave her alone and kept making fights. Only separating them in time prevented death.
Ginny managed to make Hermione take a break one time and was able to talk to her.
Hermione confessed that after Harry was arrested she had realized that had been strongly in love with Harry and couldn't feel as strongly for Ron as she did for Harry.
Ginny and Hermione started to have girl nights and got too drunk one day, leading them to become lovers after that.
They had made plans to form a threesome with Harry later. Harry and Ginny talk about Australia and then Ginny asks Harry to make love with her.
Harry visits Dumbledore's tomb and encounters Ron there. Ron sees that Harry is alive and the conversation starts friendly enough.
Harry explains how he escaped, then Ron asks where Harry plans to go and Harry tells him.
Ron's smile fades when Hermione is mentioned and when Harry goes to leave Ron stops him. He asks Harry to hand over the Elder wand and when Harry refuses to hand it over Ron goes into ranting mode.
He mentions that he wants to resurrect Hermione with the wand, because they are meant to be together. Ron has a moment of insanity and says that it was his fault she is dead. When Harry asks for clarification of that statement, Ron says that it was an accident and didn't know that the love potion he had given her would have made her react in convulsions. He brought her to St. Mungo.
There is some more insane ranting afterwards and Harry uses his wand to hold Ron still in the air. Harry uses the resurrection stone to call Hermione and gives Ron a final chance to make things right with her.
He does not and Hermione tells Harry without using words what she wants Harry to do. He resurrects Hermione with a spell that takes Ron instead. They talk afterwards.
They go to the Weasleys and tell them what their plans for life are and explain that Ron is dead.
Harry, Hermione and Ginny live together in peace at last in the end.