Amaranth Potter makes contact with an eldritch being, a mindless entity whose power is nigh infinite compared to mortals and whose intellect is entirely divorced from concepts of rational thought but is instead completely emotional, but is also emotionally detached from mortal concepts.
Over time they get close to the detriment of Amaranth's mental health, and make a pact to bring the entity into the physical world by as of yet unknown means in exchange for giving Amaranth complete authority over their power once they get there.
Amaranth becomes progressively less connected to reality in both a mental and metaphysical sense, drawing on the entity's power to achieve subtly impossible things. This all comes to a head in the department of mysteries when Bellatrix accidentally kills her while they are alone, only for her to somehow come back to life in time to steal Voldemort’s wand from the fight in the atrium. Only Amaranth and Bellatrix know about this at first.
Amaranth appears to have lost her own wand and begins using Voldemort's exclusively. Dumbledore goes to the Gaunt shack but finds it empty.
As HBP progresses, people get more and more concerned about Amaranth's mental state even as she becomes more and more focused on acquiring all of Voldemort’s horcruxes for as of yet unknown reasons. Dumbledore, increasingly worried over Amaranth's mental state, decides to try and keep from getting involved in the war and is supported in this by most people who know her. Amaranth is at first oblivious to this, focused as she is on acquiring the horcruxes, (knowledge of which she gained from the entity through its connection to her and subsequent discovery of her status as one), but when Draco lets Death Eaters into the school she freaks out and fights them, driving them off with strange powers the limits of which only Bellatrix has any grasp of. Everyone survives into DH. . Upon hearing about how Amaranth drove off the Death Eaters, Scrimgeour tries to use her as a propaganda tool and weapon but is denied by Dumbledore, who is maintaining a strict protection policy around Amaranth whose faculties of reality seem to be deteriorating in direct proportion to the increase in strange magical phenomenon around her. Her friends band together to try and help her and their presence calms her, but she also becomes increasingly agitated at the thought that anything might happen to them.
Upon being rebuffed by Dumbledore, Scrimgeour is initially angry before being contacted by the Unspeakables who say he should be more cautious in dealing with Potter. Upon asking them why, the Unspeakables take Scrimgeour down into the Department of Mysteries where they show him their newest great secret. The corpse of Amaranth Potter, along with her original wand.
Time is running out as Amaranth nears completion of her collection of Horcruxes needing only Nagini to complete the set, and Voldemort launches an attack on Hogwarts with his full forces after a diversion to the ministry. The attack goes wrong when Amaranth uses strange magics to initially repel the invaders, at which point Voldemort takes to the field. The Ministry come and set up wards around Hogwarts to prevent escape as they send in their forces, but just as Scrimgeour, Dumbledore, and Voldemort meet in the Hogwarts courtyard, something goes wrong. . A wave of wrongness emanates from the Black Lake and they all pass out. When they wake, the sky is black and light is streaming from the lake, and none of them can use their magic. They go to the lake where they find Amaranth standing on the surface of the glowing water, in which the real world can be seen reflected and they realize they are in a pocket dimension of some kind.
They then notice the strange shape, only partially real and mostly invisible, hanging in the air around Amaranth. It is the entity, and the time has come to give it a body. She reveals the horcruxes and uses them in a ritual to consume Voldemort’s soul, destroying it utterly and spending it as fuel to replace it with the entity in Voldemort’s body. The entity, which could not normally survive in the physical world even with a living body, is anchored by its connection to Voldemort’s former Horcruxes.
The horcruxes are then devoured by Amaranth in a ritual which transmutes their connection to the entity into her and her scar, which bursts open and out of which flows a strange, pale molten gold substance formed from the other horcruxes which then wraps around her head in the form of a crown, still anchored to her flesh in the scar on her forehead. . Amaranth then seizes the nearest Death Eater and has the entity reach through the Dark Mark to touch the souls of every Death Eater trapped in the pocket dimension, tearing out their souls and using them as fuel for what is to come. Dumbledore then tries to apprehend Amaranth, fearing for her life, and discovers that while everyone else's magic is bound in this dimension, the elder wand is radiating the same eldritch power as the entity and can still be used. Amaranth sees this and wields the entity's power to banish them all from the dimension, returning to the real world where she vanishes alongside the greatly changed body of Voldemort, now housing the eldritch entity.
Amaranth begins to murder every Death Eater in the country, all the people she sees as threats to her family, but all the while her mental state is decaying even further due to the now constant connection to the entity, (think Azula in the finale of ATLA). At first people think this is good, but then she kills a Ministry worker who aided the Death Eaters without knowing it and people start to realize that Amaranth isn't going to stop killing those she perceives as a threat to her family until someone forces her to.
They set a trap at Azkaban for her using Draco the bait, who had been expelled from Hogwarts after he let the Death Eaters in and was thus not present for the battle in which the majority of the Death Eaters' souls were consumed. Amaranth, now existing in a near-reasonless mental state similar to the purely emotive intelligence of the entity, sieges Azkaban in an attempt to kill the last Death Water alive whose presence she can sense due to her connection with the magic of what used to be Voldemort. . Scrimgeour wants to kill her and say she died a hero, but Dumbledore refuses. He fights her to a brief standstill using the power of the Elder wand and, after appealing to what her friends would think of what she has become manages to briefly knock her off balance, he takes a risk by plunging them both into a liminal space beyond reality where he uses the Elder wand to forcibly separate the spirits of Amaranth and the Entity, destroying her body in the process. The crown, now containing the anchors of all six remaining horcruxes as well as the connection with the original soul which has been subsumed by the entity, is cast off out of the liminal space into the depths of the North Sea, while Amaranth's soul is brought back out into reality in a form which better reflects what remains of her psyche.
Seven years later Dumbledore appears on a hill overlooking the Atlantic on the west coast of Ireland, as far from Azkaban as it is possible to get while still remaining within the jurisdiction of the British Ministry of Magic, and walks up to a small seaside house overlooking the waves.
A small girl with black hair and green eyes runs out to meet him, appearing seven or eight years old, and excitedly holds out her hand to show him something. Albus kneels and looks, and sews a small flowerbud in her hand which she causes to open and bloom with but a thought. Albus remarks how impressive that is, and how proud he is of his "niece" for achieving it. . The reincarnated Amaranth giggles mischievously and skips back out of Albus' reach, then playfully spins on the spot with arms stretched out wide causing every flowerbud in a kilometer radius to suddenly grow and blossom into full bloom, all without ever using a wand. Albus smiles warmly at her and lifts her up, using what's left of his strength while he still has it to carry her back up to the house and saying that they ought to weave flower crowns together tomorrow since Amaranth has grown so many flowers just for him, but inside he redoubled his resolve not to fail her again as he once did before.
Hundreds of miles away in the North Sea, a woman on a small Danish fishing boat pulls a strange object out of her nets, a strangely warm and faintly glowing golden crown.