Summary: AU. Years after his defeat of Voldemort, Harry Potter remains a willing and secret prisoner of the Ministry, but not all is what it seems. Harry has a plan, and the world will never be the same.

This story takes place several years after Hogwarts. You can count on books 1-5 for background information but everything after that is completely different and left to be intuited from this fanfic.

A special thanks to The Santi for the summary and the reviewers at DLP for their valuable insight and critiques.

Enjoy.

The Prisoner's Cipher

Prologue

Hermione peered down at the see-in ceiling of the prison cell below her. The cell itself was completely devoid of color - opaque really, and immaculately clean. It had been named "The Holding Room" by some of the full time guards and the name had stuck.

The room had only a desk and a cot. The Prisoner, a rather special long-term case, was told he could have three things subject to approval. With almost no hesitation The Prisoner had chosen a desk, paper, and a quill. When told whatever he wrote would be collected on a weekly basis and that the quills were to be exchanged for new ones the prisoner merely nodded in content affirmation.

Everything was granted, no harm was seen in the requests. After all, The Prisoner could not perform magic. Hundreds of wards, dozens of which Hermione herself had installed took care of that - leeching The Prisoner's magical core dry on a continual basis.

And so the prisoner wrote. Almost twenty hours a day The Prisoner scribbled with an untidy scrawl, crossing out, rewriting, and ruminating on his work. The Holding Room's guards looked with suspicion while experts from every profession looked with hope that the writings would produce the break-through they had been looking for on this high profile, complicated arrest. The air was optimistic, the nature of The Prisoner's capture leading some to believe the writings would be some sort of confession. This, however, was simply too good to be true.

In fact, it was entirely too good to be true. The writings weren't even legible - to anyone. The experts had looked at it in wonder and deep consternation, while the guards simply glared with fearful eyes.

The Prisoner had concocted a language purely of his own.

Immediately they poured over The Prisoner's work with an air of urgency and mild trepidation. The language seemed to be a cross of phonetic and syllabic languages, a cross-breed of hieroglyphics and lettering of both Muggle and Wizard background. People highly talented in the arts of linguistics, combinatorics, logic, statistics, and more spent months upon months utilizing their skills in vain on The Prisoner's cipher.

Many wished to merely dismiss the strange glyphs as the mere ramblings of a man gone insane. But the experts knew better. Anyone who knew anything about languages could see and feel the structured patterns within the parchment. There was an inexplicably brilliant and ingenious system powering the language's mechanics. Yet no one had even come close to deciphering it in ten years of fevered pursuit.

It had been unanimously agreed on by experts and amateurs alike that the language was one completely made up from scratch. Their use of prior languages gave no precedent in which to solve it. Every attempted solution yielded complete gibberish and dead ends.

The solution had to be found within The Prisoner's own past, it was the only angle the cryptologists had not tried in their vast arsenal of knowledge and ideas. Unfortunately, The Prisoner's past was so shrouded in mystery and guesswork that it was essentially as difficult to decipher as the cipher itself.

Which is where she came in. Hermione Jane Granger-Weasley. She was thought to be a metaphorical Rosetta Stone for this case. One of the most lauded minds of her generation and a key player in taking down Voldemort's forces, she truly was a force to be reckoned with. She was by no means a linguist, but she was exceedingly clever and well read. The fact that she was a researcher for the Department of Mysteries was more than a testament to this.

But other people just as clever, perhaps more, and certainly more read on the concept of deciphering languages had been on this case before her. It was not her intellect that was the main reason for her being here. It was her unique past with The Prisoner that made her role in solving the created language so essential.

Hermione swallowed thickly as she peered down once more at The Prisoner. He was sitting tranquilly at his desk, writing as though adding the finishing touches to a Transfiguration essay.

Oh how she wished so badly those days were still here. How many times had she seen The Prisoner write as he was now, brow furrowed in intense concentration, his foot slightly tapping in excess energy? Desperately getting a hold of her emotions, Hermione readied herself for a confrontation she had thought so much about but never once attempted. Not once in the eleven years since The Prisoner had been detained had she had a face to face engagement with him.

She shut The Prisoner's files with a soft finality, revealing his photo just hours after his capture. He looked feral and dirty from the campaign he had led. No injustice shown through his gleaming eyes, but a cold calculating fury demented his young, handsome features. He gazed as though challenging anyone to look into his eyes and not back down, not for help as others might have done. As those who were innocent might have done.

The Prisoner.

Number 19683.

Harry James Potter.

Chapter One

He looked good, all things considered. Really good.

He bore himself with silent confidence and a boyish charm that exuded a sense of calm and tranquility that she had never before witnessed in her first friend.

Poised but placid, a smile not quite reaching his eyes greeted her as he walked towards her with uncommon smoothness. A healthy glow emanated from his face giving her a reasonable excuse to soak in the handsomeness that the years after Voldemort had allowed him to develop.

Everything in the room was an opaque white, even his clothes. His eyes pinned onto hers with the intensity she well remembered, but glistened with a strange and foreign clarity.

Her fingers subconsciously began to fiddle, echoes of the numerous warnings resonating within her mind, both from herself and others.

"Hello Hermione."

His voice was not scratched or laden with emotion as she had so often simulated in her mind of this meeting. It was as his exterior, calm and unperturbed.

She had prepared herself for this moment, she truly had. But as the silence settled in she had a nasty suspicion that she hadn't prepared enough.

Her first undoing was looking once more at his eyes. His eyes had always been alluring, expressive when all else was stoic. Here and now they sparkled with intelligent inquisitiveness amongst a disconcerting calm.

Hermione had seizure of feelings grip her stomach – memories of the friend and person he had once been melding violently with the person she knew him to be now.

An overwhelming urge to rush and hug him wracked her body, threatening to throw all caution and professionalism to the wind. Thoughts of the job she had to do here and her husband kept her together.

Harry peered at her in a fashion that told her he knew exactly what was going on in her mind. No further emotion showed upon his visage.

"Hi Harry" Hermione said, unsure of whether she felt like she was asking someone on a date, talking to a professor, or talking to a wall.

Harry simply stared at her with a content look upon his face, "Why don't we take a seat, Hermione? A little chat for long lost friends?"

Hermione nodded, ignoring the sharp pang cutting her stomach. Wasn't she the one supposed to open up the conversation? Another painful realization quite bluntly told her that her meticulously laid out plan before coming in the room had already been long lost.

She simply had not been ready to face him again.

Harry sat in his chair in a relaxed fashion, somewhat far from the desk. His other hand played with a quill in his fingers in a slightly transfixing manner.

"I take it this isn't a personal visit, then?"

"No Harry... it isn't" Hermione replied, although she felt as though it had turned into one in the past minute or so.

"The papers then, hmm?"

"Yes."

"Then I suppose you're here to figure it out?"

She nodded. His eyes suddenly brightened considerably.

"Have you found it as amusing as I have? Eleven years... and it's still unbroken! For all they know it could be doodles."

Hermione who had looked at Harry's writings for months knew beyond a doubt they were not doodles.

"We both know they're not doodles, Harry."

"Well you of all people know I'm a doodler, Hermione..."

"Harry please, that's ridiculous, these glyphs are not doodles - "

"Did you see the one with the aardvark and umbrella? I had two interrogations over that one!" Harry laughed, and Hermione looked in wonder at his enjoyment.

"Well, yes, some of them were doodles I suppose - but please be reasonable with me Harry... you are writing something."

"Hermione I think you're being a wee bit presumptuous..."

Hermione was starting to be more than irritated at his coyness. He hadn't seen her - anybody actually - for over 10 years and this is how he chooses his facade? Already this meeting was going in a direction she didn't like. This Harry was not the Harry she once knew, but he had a frightening ability to bring back memories of what he once was.

She shook her head slightly, readying herself to just simply get to the point as civilly as she could.

"Honestly Harry, your... whatever it is, 'language' is..." and she hesitated, "amazing," Hermione responded, and she wasn't lying.

Harry gave her a pointed look as if telling her to tell him why. It was also quite obvious to her that he knew why as well.

Hermione had a sudden flashback to her as a child completing large jigsaw puzzles and her parents watching over her back in silence from the living room sofa.

When she had poured over the tons and tons of paper that had been accumulated over the years, she found herself more and more impressed with Harry's creation. She recognized a variety of patterns, but could make no clean hypothesis as to what the papers were actually saying. She had been, and still was, completely and utterly stumped.

She had initially thought it would be simple. Cryptology was an ancient and well established field. Yet the patterns that she intuited from Harry's work defied all of the codes from the literature and belied something new entirely. She had intuited some of the underlying principles of the language but could make no more headway. The burning question in her mind from the past six months came out at last.

"How did you combine mathematical rhetoric with something as arbitrary and unstable as a language? Harry... I know you're placing letters or sounds with mathematic rules to construct your sentences. I just don't get, at all, what the symbols represent - There's barely any consistency, they change! Even from week to week!"

And she really, really did want to know. How had she missed this type of intellect in Harry? What further ingenious machinations were the writings depicting? How much had he hidden from her, from Ron... from everybody? What had happened those last few years before he'd been taken in?

Harry took her academic tirade in stride, as he always had. He had begun to scratch something on a paper in front of him with slow methodical strokes.

"How are you and Ron?"

Hermione blinked in surprise at the turn of topics, unsure of how to respond. A nagging part of her wanted her to lash out in anger, for him betraying her and everyone like he did. But the way he sat at the desk... so passive and dressed in prisoner's garb, stayed her mouth, moving her feelings dangerously close to pity.

The guards had instructed her to take off her wedding bands so as to not give Harry any sort of verbal ammunition or information, but she supposed his observation was merely the obvious.

"We're... we're very happy."

"I'm glad, very glad... and I'm guessing he went on the Auror side of things, rather than Quidditch?"

Hermione's eyes widened slightly in surprise, "Yes... he did. It was a very hard decision. How did you know? Did someone tell you?"

"Come now Hermione, you know I'm not allowed news in here."

"Then how did you know?"

He pointed casually with his quill at her arms. Her heart clenched in realization of what he was referring to.

"You have a rather sloppy stinging ward placed on your lower arms. No one bothers to cast those but Aurors, and Ron's always missed the subtleties when it comes to casting the more meticulous branches of magic. So his 'signature,' so to say, is quite easy to spot. It's very sloppily done. You should have done it yourself, we both know you could cast a better one... Thank goodness I'm not the violent type, I doubt that ward would do much harm."

Hermione stared at him in wonder, seeing him not for the first time this afternoon, as if in a new light. A retort was on the tip of her tongue that would curtly point out that he was the violent type but Harry interrupted her before she could start.

"In fact, the very idea that you let him cast and kept such a dismal spell - that I know you know is subpar - speaks volumes of your relationship with him. The person who makes Hermione Granger consciously outfit herself with lamentable mediocrity must be a special man indeed! I congratulate you both," and he looked up momentarily from his drawings to give her a quick handsome smile.

When she recovered, his face was once more buried in concentration in whatever he was scribbling. Despite her rising anger, she could not help but ask her initial worries.

"Harry..." she intoned slowly, "how did you detect that spell?"

The very idea of him able to use magic made her more than a little bit uncomfortable. She had seen first-hand the power and cold violence he could commit. She was given an obscene amount of warded objects to wear by the guards that would probably kill him if he tried any sort of physical attack, but it still did not quell the needling feeling of fear in her chest. Perhaps she should have cast the stinging hex herself... and the others Ron had insisted he put on. No doubt Harry knew of those too... somehow.

"Living for ten years in the absence of magic leads one to be, if I may say so myself, exceptionally in-tune with the precious few encounters of magic I may have."

"By the way, you're part in the boxing ward placed on this cell is exquisite, Hermione. It's a beauty, for sure."

Hermione stared. She was beyond uncomfortable. She needed to get what she came for and get out. The things he was saying... they belied a power and intellect that was cunning and immeasurably sharp and she was completely unprepared for it. She was clearly out of her element and he was playing her like a masterful concerto.

Nothing was going to come out of this meeting for her own personal closure, and the chances of her getting something out of it as a professional were slim to none. She decided to give one more try, and leave. There was nothing to be gained here but pain.

"Harry I just need you to tell me about your writings. Then I can leave you alone, they can leave you alone."

"I've been alone almost all my life Hermione, and never more than now. Why wouldn't I want your company?"

Her eyes narrowed, "This time it's of your own doing Harry, I know what you did."

"Oh, do you?"

"I know so, Harry. Then and later when I testified under oath and Veritaserum."

"Oh yes, how easy it is for me to forget..." by this time Harry had set down his quill, an intricate drawing with some sort of inscription above it was showing, but she couldn't quite see it clearly behind his arm. He seemed to have finished it. He was smiling but she could feel the tension build to higher levels than before.

"You and Ron, of course I remember... a crowd favorite too... did so well together in the court room... rather indicative of what's become, don't you think?"

Hermione stared, at a loss for words.

"You know, Ron's speech had some pretty big words in it, you didn't happen to have a hand in that did you...? Not like any of your testimonials did anything in the end anyhow..."

She had of course, and she squirmed under his penetrating speeches, but she fumed at the fact she had entertained such cherished and warm memories and thoughts of him earlier.

"Harry just give me a single clue, a single affirmation as to what the hell at least one of these symbols mean! The sooner you give me something, the sooner I can get the hell out of here, figure out your 'language,' and never come back."

She wanted her speech to hurt him, as his words had done to her. But her tirade was a dull butter knife as his was a precise and finely tuned carving knife. Harry merely smiled wantonly and reclined slightly in his chair peering at her just above his glasses.'

"No... no no, I don't think so. I rather like entertaining the thought of you not knowing something that I had made up in a matter of seconds. I mean... it's your fault you can't decipher it anyhow," he finished, chuckling at the end.

And what was that supposed to mean? Hermione was brimming with anger but managed to simmer, "What do you mean my fault?" she said with a dangerously low tone.

Harry leaned a little across the desk with childlike mirth in his eyes, Hermione forced herself not to consciously back away.

"Meeting with me might flare up a couple undercurrent feelings of jealousy in our red-headed compatriot, yes? You, still having to devote your attention to me even after all these years... truly a pity, I do apologize."

Harry locked eyes with her as if making sure she was listening, and continued.

"I mean... a little court testimonial bonding doesn't fix every kink in a relationship, yah? Snakes have fangs, while dogs have teeth, but Big Boy Red here has the blinding surge of jealousy for his lethal bite. I'm guessing you and Ron will have the customary spat over this meeting, correct? "

Hermione would rather eat a dead mongoose than admit his correct assumption.

"No no... no need to answer that as well, Hermione... it is rather rhetorical after all. All I'm saying is that this time when you two get to 'making it up,' you avoid the kitchen counter as you did last time. Merlin knows the things that must fly out of Ron's mouth when eating there... Hygiene my dear, Hygiene... I shudder at the thought..."

Legilimency! He had used Legilimency!

Hermione fumed and immediately stood up, knocking over her chair in the process.

The lights flickered dangerously in the room, and she immediately felt drained and weak. She immediately recognized that she had done accidental magic. She heard the guards burst in the room and make to cart her off.

All she could see was Harry, who hadn't moved from his position, still calm as ever behind the large opaque desk. Her hateful glance burned at him, willing him to combust on spot. A bemused smile sat contently upon his lips.

Her voice was weak from the magical deprivation but hissed venomously, "You're a bloody murderer, Potter, a murderer and a terrible person that's no better than the murderer you put down!"

Harry merely cocked his head, her lashing statements evoking no other emotion from him.

A small quaint smile graced his lips as he worded his reply with tantalizing annunciation, "Don't forget to shut the door, Hermione. Ignorance has a nasty habit of finding its way into the conversations that happen here."

Even in her hate she recognized the oddness of this statement and her eyes sought his, despite her fears of being subjected to his Legilimency.

The intensity in which his eyes met hers took her breath away. Unable to look away she saw his eyes shoot a pointed look towards the desk.

The realization barely made it through her red haze.

The paper! It was gone... Where had it - ?

Harry, ever so slightly, nodded towards her left pocket. The paper, neatly folded, was just visible coming out of her pocket.

How...

Somehow, Harry had managed to slip the piece of paper in her pocket during the distraction of her anger... He had to have used magic, there was no other way, it was not possible to have been done so physically.

How?

Her eyes caught his one last time, showing not only her astounded confusion, but her awareness of the act that had happened.

Her hand pushed the paper further into her pocket as the guards took her out of the Holding Room, her mind reeling from the events that had unfolded. The guards were peppering her with questions but her mind simply was not up for the occasion.

All she knew was that she had come out with a lot more questions then the answers she had come in looking for.

Suddenly she froze as an epiphany hit her, causing the guards to stumble into her, still waving their wands distractingly to dispel the numerous wards on her body and the objects she carried.

"Finally!" yelled a nameless Ministry witch, "We've asked you to stop walking ages ago!" but Hermione didn't care in the least.

She stared for a half second at the hand that had just pushed down the paper. She had not just pushed down one paper, but many. Harry must have put the ones she had been watching him write earlier with the one he had completed while talking to her.

Her heart in her mouth, she quickly answered the guards' questions without once betraying her knowledge of the papers in her pocket.

She wrapped her coat around her shoulders in a protective, shielding manner as she desperately tried not to ask herself why she was hiding what Harry had given her.

She had to get home.