This story is borne from a prompt posted in the HG/MM Facebook group an absolute age ago, by Sela McGrane. The prompt was a picture and the following info (I will post the picture - credit to Sela McGrane - if/ when my computer stops being a cock):
During the Battle of Hogwarts, Minerva does something which Hermione does not think she could forgive. This can be anything except the typical "Hermione is rejected by Minerva". At the point of the Battle of Hogwarts, Hermione simply has great respect for her mentor. Years later - I'd say at least five, though could be as much as twenty-five - Hermione, who now works for the Ministry and is on the Educational Board, is sent to Hogwarts to evaluate if Minerva, the Headmistress, is adequately running the school. Minerva is rather peeved at the Ministry interfering, and less than pleased when she discovers that it is her once favourite pupil, with whom she had a falling out, that is sent to evaluate her. Heads butt as Hermione tries (and fails) to find flaws in Minerva's methods of running Hogwarts, and eventually there is a confrontation in which they talk about what happened to end their good relationship. After that, it's only a matter of time before they realise that the feud only hurt as much as it did because there were more than friendly feelings brewing back then, even if neither of them realized it. What will they do about it now?
So... yeah. At least a year later, and so it goes...
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Hermione wandered out of the Great Hall, her footsteps reflecting the numbness that her brain was emanating. She needed to get away; away from the constant crying, the sobs, the deathly silence surrounding some. Harry felt the same, she knew. She had covered for him when he had slipped away, not asking where he was going, just understanding that he needed time to absorb, to begin to come to terms with the events of the last few hours. She understood, even if she couldn't know exactly what he was going through. They were part of the Weasley's family now, of course she knew this, but it was different, seeing them all there, huddled around Fred's body, holding each other. They had grown up together, built their family together; she – and Harry, she supposed – needed to deal with their own feelings before becoming embroiled in their adopted family's.
She nodded to Madame Pomfrey on her way out – the matron had looked as though she were about to approach Hermione, but a small hand on her shoulder had stopped her from rising. Hermione was grateful to Professor Flitwick for the intervention. She swiped at the small amount of blood gathering on her brow as she continued walking through the rubble, dismissing the small gash. People had suffered worse. She headed towards the entrance doors, intent on some fresher air, when a noise to her left caught her attention. She froze, trembling hand reaching towards her pocket as a million thoughts raced through her mind in a single second. That room, off to the side, was where they had put the bodies of the Death Eaters, of all Voldemort's followers. Voldemort himself. Her jaw clenched of its own volition as she took a step towards the open doors, steeling herself for another confrontation, not sure if she had enough stamina left to keep her upright, let alone enough to fight.
Hermione took a hesitant step through the doorway, trying to ignore the smell of blood and death and convincing herself that the room wasn't exuding hatred. Her eyes scanned the immediate vicinity, and seeing nothing untoward she took another step. The sound pricked her ears again, and she immediately turned towards its source. A gasp tore from her throat, and her wand clattered to the floor, forgotten, as she took in the scene before her.
Minerva McGonagall's head snapped up as the sound of the wand hitting the slate floor reverberated around the room. A part of Hermione's mind – the part that wasn't reeling from what she was seeing – was shocked at how dishevelled the always-composed Professor looked, at how she scrambled to her feet, her bun flopping with the movement, but it was overrun by the part that was witnessing Minerva McGonagall, her beloved Professor, Mentor, Leader of Light, cradling the head of Bellatrix Lestrange, one hand gently laid on her chest atop a black rose, her face almost buried in the manic locks.
"NO!" A strangled cry.
"Hermione-" Minerva reached out, once she had found her footing, her face etched in pain and worry. But Hermione had already stumbled backwards, out of the room and into the corridor. Before Minerva could move any further, Hermione had run.
Minerva followed Hermione's scent, a task not made any easier by the amount of smells mingling within the castle at the moment. Minerva had been momentarily surprised that Hermione hadn't bolted straight outside, but nevertheless had followed the trail until she came to a halt in front of the Headmaster's – hers, she corrected, absently – office. Ignoring the moans of the partially smashed gargoyle, she picked her way up the stairs that were just visible, grateful that it seemed as though this room had remained unsullied by the dark magic that had tried its best to permeate the castle. Hermione whirled to face her as soon as she fully entered the office, fists clenched by her sides, face beet red, adrenalin obviously coursing through her body. Minerva came to a stop, noting quickly Hermione's position underneath Albus' portrait, and also that he was still, blessedly, asleep.
"I… I came here for help…"
Minerva knew why Hermione had run to the office: sanctuary. Someone to sort out the problem. Someone who could provide answers. For a moment, Hermione looked helplessly lost, and Minerva's heart ached for her: Never before had the school failed to provide solace for the younger woman. However, Hermione soon remembered who she was talking to and she put more distance between them, her hand fishing in her pocket. Minerva held out her own hand.
"You dropped it," she said, moving closer to Hermione and holding her hand out. Hermione eyed her cautiously before moving forward to grab her wand and promptly taking a few steps back again, pointing her wand towards Minerva.
"Were you ever taught that you shouldn't point your wand at someone in anger… Unless you have a genuine reason, of course?" Minerva enquired, trying to catch her breath.
"Yes," Hermione answered evenly, though her arm shook. Minerva nodded.
"Very well. Hermione, what you think you saw-"
She was cut off by Hermione's bitter laugh.
"What I think I saw?! Please, then, Professor-" Hermione made it sound as though she almost choked on the word, and Minerva flinched. "-pray tell, exactly what was it I actually saw?"
Minerva sighed, pushing loose strands of hair away from her face.
"It wasn't what you think. You wouldn't understand," Minerva stalled, wondering where to begin, and more to the point, how to end this conversation with a quick, positive outcome. Her head throbbed, and her chest felt as though it was on fire. She suspected broken ribs, and a warmth spreading down her leg was a definite sign of an open wound.
"Then explain!" Hermione shrieked. "And quickly."
Minerva's hand fell to her hip, where she had located the source of the bleeding.
"Not everything is black and white. Especially in times like this. Look at Severus Snape."
Hermione blinked, disbelieving.
"Are you trying to tell me that Bellatrix Lestrange is some kind of hero now?"
"I'm not trying to tell you anything. Please, Hermione, just for the moment, can you trust me, trust your faith in me? You're raw, I'm weary: can we revisit this tomorrow?"
Hermione backed away. "You're weary? Not weary enough to bypass a visit to the Death Eater morgue. To forego cosying up to the body of a certifiable lunatic! What the fuck, Professor?! What, is she your… friend?!" Hermione spat.
Minerva flinched, whether from pain or shock or guilt, Hermione didn't care.
"I can't explain. Not right now. I just need you to trust me. It's not what you think."
Hermione violently shook her head and her wand hand.
"That… that woman tortured me. That woman, who's hair you were stroking, into whose ear you whispered sweet nothings, she bound me on the floor of Malfoy Manor and tortured me."
Minerva paled.
"Hermione, I…"
"No!" Hermione screeched. "You don't want to explain, remember?! Or are you going to offer excuses for her now? Things aren't always as they seem?" Hermione laughed bitterly as she tugged her jacket sleeve upwards, revealing a bloody mess to Minerva, the word 'Mudblood' prominent, sealed as it was with Black magic.
"How does this seem to you, Minerva?"
The hammering of her heart was all Hermione could hear as she watched Minerva's face crumple. Minerva reached out to Hermione's arm, but Hermione pulled away, yanking her sleeve down.
"Don't come anywhere near me," Hermione's voice was the lowest and coldest that either woman had ever heard. Minerva stopped dead. "I should go to the Aurors."
Minerva momentarily closed her eyes. She could feel her strength waning.
"And tell them what, Hermione? I protected the school, protected the students…" Protected you remained unspoken, though heavily implied in the glare that Minerva pinned Hermione with. "I have done nothing wrong."
"Well there's obviously something that you're hiding!" Sparks flew from the end of Hermione's wand as her emotions became barely containable. Minerva tried to breathe evenly, her chest feeling tighter by the minute. She needed respite, before the pain racking her body made her responses something she would regret.
"What you witnessed… What you witnessed was something I need not justify. Whatever is going through your mind right now is pure conjecture based on your rage. You are not in possession of the full facts. Nor will you be at this moment. Now, you may go to the Aurors if you so wish. But I will not be seeing them until tomorrow, at the earliest. And even then, I shall still be Headmistress of what's left of this school, and I will have an insurmountable task to undertake in the rebuilding of bricks and mortar, and spirit. I'd rather not spend my time recounting my every insignificant action, when any investigation shall come to nothing."
Try as she might, Minerva couldn't help but stumble over the word 'insignificant', something that Hermione picked up on.
"You'd lie to them… like you're lying to me, now?" Hermione asked, incredulously.
Minerva set her jaw. "There are things that you, even you, will never know. Do not need to ever know. I am sorry you do not have enough faith left for me," She gave in, and steadied herself with a hand on the desk, her other hand moving to cup her ribs. "But leave it be; it'll only cause more heartache."
Hermione stared, her wand lowering as Minerva slumped further into herself.
"Are you threatening me?"
"Warning you," Minerva answered through gritted teeth. "I am sorry, truly sorry about what you have gone through; what all my students have gone through. But there has been nothing between Bellatrix and I that would have enabled me to change anything. I was merely… saying goodbye to someone I once knew. I would have explained… tomorrow."
Hermione searched Minerva's eyes for a long moment, trying to look past the pain she found there. Minerva eventually looked away. Hermione made her way to the door, stopping just close to Minerva.
"I'm sorry I trusted you."
Hermione's crackling magic ensured that the door slammed behind her. Minerva, for her part, wanted to follow, but her wounds ensured that after one step towards the door, she inadvertently cried out and crumpled in a helpless heap.