Author's Note: I'll do my best to keep this brief, I'd like to keep Author's notes at a minimum and let the story speak for itself. I have just a little bit of background for you, which should be explained in the story eventually through exposition or perhaps a few flashback chapters.
In this story, James and Lily's child was a girl, named Harriet (or Harri) Potter. The Dursleys chose to send her to a girls school to keep her freakishness away from Dudley. There, she met Hermione and they became friends. Because the two spent so much time together, any accidental magic that Hermione performed was attributed to Harri, and thus she was not recognized as a muggleborn. The two remained close friends, though they could only see each other over the summers, until our story begins, the summer before Harri's 5th year.
About how I plan to tell the story: This might be a little more episodic than most long-form stories. I may jump a little ahead, or interrupt with flashback chapters. The goal is keep the story flowing forward and also to avoid simply retelling canon parts of the story.
"Hermione, just run, run as fast as you can back home. I need you to trust me, and get away from here." Harriet Potter tried to keep her voice calm, but fear was creeping into her voice. She could deal with a dementor, probably even two of them, but having to worry about protecting her muggle friend while doing so was more than she wanted to deal with right now.
"Harri, what's going on?" Hermione asked, feeling some sort of disturbance, but unaware of what was causing the hot summer day to feel cold, the light of day to dim, and the sense of dread enveloping her. "I'm not going to just leave you here, you need–"
Suddenly she stopped and shrieked at the top of her lungs. In front of Harri two masses of black robes appeared and floated towards them, and the ominous feeling mirrored their advance. "What are those things!?" Hermione yelled in terror.
"Wait, you can see them?" Harri turned and asked in disbelief, for a moment forgetting the danger they were in. Shaking her head and returning her thoughts back to the monsters advancing on them, she pulled out her wand, another surprise for Hermione.
Now speaking with all the conviction she could muster, Harri tried to impart just how severe the situation was to her friend. "Hermione, you need to run. I can hold them off but this is not something you can deal with. More than anything else I've ever told you, I need you to do this right now and not question it."
"Promise me that you'll be okay, Harri," Hermione pleaded.
"I will be, just go! I promise."
Hermione nodded, and trusting that her friend would be alright, she did as Harri said and ran. As she left the confrontation, she could see Harri waving around the stick she had pulled out of her pocket to somehow create a silver apparition which seemed to hold the monsters at bay. After that, she didn't look back.
When she reached home, out of breath and completely spent, she tried to explain to her parents what had happened. It seemed far-fetched, but Hermione wasn't one to make up stories, and she seemed absolutely convinced. Her parents grew even more suspicious when, after calling Harri's aunt and uncle, they learned that Harri hadn't been seen or heard from. That was the answer every day until eventually the Dursleys would simply hang up whenever one of the Grangers mentioned their niece. Hermione had even gone so far as to travel to Surrey to try to find her friend, but no one had seen her, and Vernon slammed the door in her face when she tried to ask.
A week later, no less concerned about her friend's well-being, but now out of ideas of how to check up on her, Hermione was surprised by an old man wearing a strange set of clothes on her way back from school. "I understand you are a friend of Harri's, yes?" the old man said softly.
Hermione was rather wary of this strange man, but her worry for her friend far outweighed her apprehension. "Yes I am, do you know what happened to her? Something strange happened and now I have no idea where she is," she replied cautiously, not wanting to give away too much information to a complete stranger.
"Strange, you say. Perhaps something magical? Follow me," the old man said and walked a bit out of the way, into a small park away from where most people would pass by. "Now this may be a bit of a shock, but your friend Harri is actually a witch."
"A witch!?" Hermione interjected. "How can you say that? Harri is the nicest person I know, there's no way she could be a witch."
"Ah forgive me, sometime I do forget how we may come across to those without magic. A witch is simply the term for a female who can use magic, and for men like me, a wizard," he said, snapping his fingers and producing a steady flame above his hand.
Hermione was absolutely fascinated. She had millions of questions to ask and was about to ask all of them at once until he started to speak again. "I know you may have many questions for me, Miss Granger, but for now I need your help to aid your friend Harri. There is a law against using magic in the presence of those who do not have it themselves, and she is about to be tried for it, and could be in quite a bit of trouble."
"But she only did that thing to try to protect me!" Hermione shouted in protest.
"I know Miss Granger, but some others might not see it that way, some may have… biases against your friend. But if you come with me, just for a few moments, we should be able to help her. Now, please take my arm."
Eager to help her friend, and also to learn more about magic, Hermione did as he said, and as soon as she touched him, they vanished. They reappeared in a large hall, filled with bustling people, all wearing the same strange clothes as the old man. She followed him to an elevator and down eventually to what seemed to be a court, with stone rows rising up around them and surrounding them.
One of the figures seated in front of them called out, "Dumbledore, what is the meaning of this? The trial is not for another hour, and who have you brought along with you?"
"Some new evidence has come to light that should quickly resolve this case," he said with a faint smile. "Standing before you, is the supposed muggle in front of which Miss Potter cast the patronus spell. You claim no other muggle witnessed to her crime, correct?"
"Correct… however–" the same figure replied, only to be cut off by the old man, whose name she now knew as Dumbledore.
"Then the case against Miss Potter has no merit, because Miss Granger here is not a muggle, but in fact a witch."