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When the sparks finally dissipated, there was no blood visible on either of them, and the rune on Hermione’s chest was only a faint white scar.

"Thank you, sir," Hermione said, and when she smiled, the tears started flowing freely down her face.

Far to the north, in the fortress of Azkaban, something subtle happened. It was a sympathetic reaction: a slight tingle, nearly imperceptible, in a Gebo rune forever etched over another woman’s heart.

Bellatrix Lestrange stirred in her sleep.

I hope you enjoyed that last little glimpse of the narrative. I have a few more things to share with you before I say goodbye.

First, a quick note on how Hermione described Harry. The way Hermione understands Harry—that he doesn’t really have friends, only tools—is how Harry understands himself. But that’s not the way Luna understands Harry, and the way Luna understands him is the way I understand him. Harry does genuinely love his "tools"; that is the "fondness" Hermione speaks of. Hermione and the others really are his friends. He also genuinely feels compassion for people who are being hurt; it’s why he steps in when he sees bullying. But he struggles to process these feelings without rationalizing them through the lens of his three rules. It’s not clear if he will ever free himself from these constraints. (Though perhaps the certainty and permanence of his tie to Hermione would help him to let her in more.)

Luna understands this immediately when Harry approaches her because she has been keeping an eye on him throughout the year to that point. She trusts him because she knows that, underneath his mercenary explanations, he is ultimately motivated by real concern and warmth.

Second, some ideas about where the plot would go from there:

Harry would be unimpressed by the Order of the Phoenix’s passive approach to the war and would ultimately conclude that Dumbledore’s leadership was an obstacle to victory. Instead of building the DA, he would start building a sort of non-blood-purist equivalent to the Death Eaters, using similar organization and tactics but serving the cause of Muggleborns, non-humans, and allies.

Harry would agree with Dumbledore that making seven horcruxes was absolute madness, but I think he would actually conclude that making one would be a sensible insurance policy. He might do it by killing Dumbledore after he’s weakened by the cave. His horcrux would be an unremarkable rock, dropped in the sea a few miles away from some random shoreline.

Harry would not bother returning to the Dursleys after sixth year. He honestly wouldn’t care if they were protected or not.

Once Dumbledore was dead, some OOTP members would join Harry’s organization, but not all. Fred, George, and Ginny would definitely go along with it; it’s unclear how many of the other Weasleys would. They might end up being left in the cold.

Harry’s reputation with the goblins would help pull them into his camp. Gringotts would end up bending or changing a number of rules to bring about the destruction of the cup.

Harry would also do some very creative things with Dobby. If "a house elf that is bound to a wizard is also bound by wizard laws", that implies that a house elf that is not bound to a wizard is not bound by wizard laws. For instance, anti-apparition wards usually allow house elves to pass through them so the household staff can move around unseen; other families’ elves are still unable to trespass because they are bound by wizard law. But Dobby isn’t, so he can pretty much go anywhere and do anything, and nobody really thinks about house elves or notices their presence.

Harry’s org would probably do their best work after the Death Eaters had taken the Ministry. It would notably include a campaign of assassinations targeting members of the Muggleborn Registration Commission, which would hinder its efforts and ultimately frighten people into avoiding working on it. The muggleborn genocide would not progress as far as it did in canon.

In the final battle, Hermione would duel Bellatrix one-on-one and prove her equal. (Sorry, Molly.) However, both are functionally immortal as long as the person they are bound to still lives, so Bellatrix would die when Harry killed Voldemort.

After the war, Hermione would be the public face of the new pro-Muggleborn leadership of the Ministry, but it would still be Harry calling the shots behind the scenes, with their control of the government maintained partly by threats of violence. Harry would publicly basically just be a househusband, but his responsibilities would weigh on him significantly more than they did in the Mirror of Erised. Not quite what he dreamed of, but it could have been much worse.

As for the romantic entanglements...well, I’m sure Harry would at least sleep with Hermione a few times—it would just be too tempting for him, and she wouldn’t mind it one bit—but I’m not totally certain which ships would ultimately come in. My best guess is Harry/Hermione/Luna, though. (I doubt there would have been really explicit scenes in any case.)

Next, some random notes that don’t really fit anywhere chronologically:

Dean owes Harry a favor for the knife.

Harry has the Map but doesn’t know what it is yet.

Harry would eventually steal one of the Keys of Hogwarts from Hagrid; I didn’t come up with a specific place to fit that, though.

Hermione habitually regurgitates a thesaurus while insulting someone, with each word related in some way to the one before it, all without ever swearing.

Harry should end up with one heirloom of each type. He still needs something that "was crafted by a member of one generation of a family and then given to a member of the next generation".

Goblin silver is no better at surviving Killing Curses than any other material—the Killing Curse dissipates but explodes the object. However, Harry recognizes that, contra the usual descriptions, this actually means the Killing Curse absolutely can be countered: You just have to put a solid object between you and the curse. Harry should endlessly drill summoning and conjuring solid obstacles to block Killing Curses, including wandless summoning, until his reactions are fluid and effortless; this would stymie a lot of Death Eater combat styles.

I chose the symbols on Harry’s three throwing knives intentionally, and each matches its role later in the story. The shield is unpoisoned; it’s the one he ends up using most of the time in two-handed defenses. The dragon is poisoned with sleeping potion, as a nod to the Hogwarts "draco dormiens" motto. The Potter family motto one—"no better friend, no worse enemy"—is poisoned with basilisk venom because, well, there is no worse enemy than that knife, is there?

Once he gets the sword, Harry adopts a variety of two-handed fighting styles: sword and knife (with the knife parrying), knife and wand (with the knife parrying again), and sword and wand (with a fluid mix). That last style is especially hard to combat, as the sword has enough reach that he can attack and defend with either hand. Combined with his athleticism allowing him to dodge many spells, he is a very difficult opponent for most wizards to handle—even Voldemort struggles to deal with the sheer amount of crap Harry can force him to deal with.

It’s possible that once she is bound to Harry, Hermione would actually be susceptible to orders from Voldemort until they were separated. (OTOH, that would mean Harry could order Bellatrix to do things, so maybe not.)

It’s possible that Harry’s good relationship with the goblins would lead to him getting a goblin warrior name (or perhaps that he already had one). It’d probably be "Spellscar".

Ninety-Nine Charms the Ministry Doesn’t Want You To Know also contains instructions to break the Trace.

The Ministry of Magnates was written by Dumbledore. He wrote the chapter about himself to prevent speculation that he might have written it, to slander him in the way he wants his enemies to think of him (doddering and out of touch, so they underestimate him—rather than, for instance, secretly connected to Grindelwald or deeply manipulative, which would be more disruptive to his political goals), and to deepen Snape’s cover by making it appear that Dumbledore’s trust in him is a mistake.

One of the books in the Healing teacher’s office that Harry couldn’t understand in first year includes information that would help in separating Harry from the horcrux in his scar.

The magical carvings in Harry’s bookcase—the ones that are based on the books shelved nearby—include the deathly hallows symbol because of the copy of Beedle the Bard that activates the portrait.

Secrets and Lies is a little inaccurate when it implies that only the third form of Occlumency changes your personality. In fact, all three do: the first one (Dumbledore, Voldemort, Snape, Hermione) tends to make you colder and more calculating, the second (Harry) tends to make you more temperamental, and the third (Luna) tends to make you more prone to dissociation. There is no good way to practice Occlumency—restructuring your mind in order to shield your thoughts is fundamentally detrimental to your mental health.

The "tiny monograph on house elves" is setup for shenanigans with Dobby later. If Hermione seems ready to veer into SPEW-land at some point, I think it would also be used to alter her approach.

Not all magical retailers are in wizarding districts like Diagon Alley or Hogsmeade. For instance, there’s a shop on the Canterbury high street (near Hermione’s home) called "Pure Magick" which appears to Muggles to be a new-age store, but actually has a back area that carries real merchandise for wizards. This sort of thing is actually pretty common, with dozens of little magical businesses like this hidden throughout Britain.

As a general theme, I wanted to set up somewhat unnerving parallels between Harry’s side and Voldemort’s. Harry isn’t really a good guy, just better than the alternative. You see this as early as Chapter 2, where Harry talks to Dumbledore in his bedroom much as Tom Riddle did, and they even discuss some of the same topics, but Harry’s answers are a little more justifiable.

If Harry parallels Voldemort, then Hermione parallels Bellatrix—much saner and typically kinder, of course, but no less committed to Harry than Bellatrix is to Voldemort, and no less dangerous to his enemies.