Disclaimer: JK Rowling owns Harry Potter. Nicolas Flamel is kind of fuzzy as a fictionalised representation of a real person.
Update: After much consideration, I've decided to put this story up for adoption and/or co-authorship. By this, I mean that I am releasing it to the community for anyone who wants to write a continuation, sight-unseen, but I am also willing to beta-read or otherwise provide input into the continuation, including doing a little bit of the writing. I only request that if you choose to continue it, you keep it rated T and maintain a reliable update schedule. Please PM me if you are interested.
The reason I am doing this is that I no longer believe the story is a good fit for me. I wanted to make it two or three times faster-paced than my other stories, covering 3-5 years of time in only 40 chapters, plus I never had any clear outline for the story. So while I still like the idea, at the end of the day, I don't believe my writing style matches my vision for this story, and I'm not keen on yet another Hogwarts years rewrite anyway, so I think it's time to give it up. Rest assured that this is not reflective of my writing in general, but only of the unique problems of this story.
Prologue
Harry struggled to keep Quirrell away from the Philosopher's Stone as the man screamed in pain, and the face of Voldemort on the back of his head kept shouting, "KILL HIM! KILL HIM!" His own head felt like it was on fire. He felt Quirrell's arm being wrenched from his grasp just before everything went dark.
The next thing he knew, Harry was lying on something soft and slowly blinking awake. He didn't know what had happened. All he knew was that the first thing he saw clearly was a pair of piercing blue eyes.
He blinked again. The eyes were not set into the face of Albus Dumbledore. In fact, they belonged to a man he had never seen before. He was a young man—younger than any of the teachers, maybe in his late twenties. He had a round, kindly face, but a rather long nose. He had light brown hair that he wore long, but with a strange haircut—shoulder-length on one side, but only falling to his chin on the other.
"Hello, Harry," the man said in a soft voice, leaning over the hospital bed. "My name is Nicolas Flamel."
Harry's eyes almost popped of his head. "Mr. Flamel!" he gasped. "I'm so sorry! It was Quirrell! He got the Philosopher's Stone—!"
"Calm down, Harry." Flamel's voice sounded even more grandfatherly than Dumbledore's as the young-looking man reached out and laid a hand on his shoulder. "There is something you need to know…There is no Philosopher's Stone. There never was."
"Wh-wh-what…?" Harry said. His brain couldn't process the words. They didn't make any sense. "Th-there's not…? But…but that book Hermione found—it said—"
"That I am well over six hundred years old. Yes, I am, but not because of alchemy." He chuckled a little. "Even muggle historians will tell you that I didn't become famous for alchemy until two hundred years after my supposed death."
"Then how—?"
"The Elixir of Life," Flamel said, "is not created by alchemy, nor is it commonly known by that name. I would not expect you to know of such things at your age, Harry, but there is a potion called the Polyjuice Potion, which allows you to take on the appearance of another for a period of time. All you have to do is add a piece of that person, usually a strand of hair. You will take the form of that person exactly as he was when you took the hair from his head."
Harry nodded in understanding: "So if you took a hair from a young person…"
"You would become young like them for as long as you took the potion, yes. And it can do more than that. Not only does it turn back the clock, but for many serious injuries, a dose of Polyjuice Potion primed by an uninjured person will repair the injury long enough to get to a Healer. It's saved my life several times that way in addition to my regular usage.
"Now, certainly, I could have taken hair from some other young man—or woman, for that matter—and I often have, but it always feels more natural, and is safer, to be in my own skin. This is my original face, in case you were wondering. You see, every six months from the time I was twenty-five to the time I was seventy-five, I cut my hair and saved it for use in the Polyjuice Potion. Polyjuice comes in various strengths, but the strongest form lasts for twelve hours. In that case, a full head of hair provides enough to last for a century. The only downside is that each hair retains a memory of being in the middle of that haircut." He motioned to his strange hairstyle, which Harry now recognised as being cut on only one side.
Harry was in awe, his mouth hanging open. He knew magic was powerful, but even so, the Philosopher's Stone and the Elixir of Life had seemed like some distant fantasy, not something that could be mass produced. If he'd known what could be done with ordinary potions, he would have tried a lot harder to work past Snape this year. It took a couple of minutes for words to come back to him. "You mean, you can live for thousands of years just on your own hair?" he said shakily. "Why hasn't anyone else done that?"
"Oh, many have, but most fail. You have to drink the potion every twelve hours without fail, never getting a bad batch, never losing it or having it stolen, never oversleeping and missing a dose, for hundreds of years on end. Changing back to a six-hundred-year-old man won't make you turn to dust, but it will probably kill you before you can get some more potion. Perenelle and I drink the potion every eight hours just to be sure, and we always have at least three overlapping batches brewing at once, and even then, we have had some very close calls. Most who have tried this method died before they reached two hundred."
That made a surprising amount of sense, Harry thought. If cheating death were easy, everybody would do it. Still, that wasn't the only thing the Philosopher's Stone was supposed to do. "What about the gold?" he asked.
Flamel chuckled: "That was the easy part. I've been investing in gold mines since the reign of Louis XIII."
Harry actually laughed. Maybe he was getting spoilt thinking there was a magical explanation for everything. But still, now that he could make sense of the situation, something was still troubling him. "Mr. Flamel," he asked, "did Professor Dumbledore know there was no Philosopher's Stone?"
At that, the old man sighed: "I'm am sorry to say that he did, Harry."
"Then he knew—"
"That there was no danger? Yes. But I am afraid it is worse than that. Harry…you were set up from the start."
That threw him for a loop more than anything else "What do you mean?" he said.
"The only real protection on the false Stone was the cerberus, and Hagrid, bless him, is not good at keeping secrets. He was all but certain to tell you how to get past it. The rest of the protections could be beaten by any competent fourth-year student with a good chess game. The entire dungeon was set up as a lure for Voldemort—and for you."
"For me? But why would Dumbledore want to get me and Voldemort together?"
"There is a prophecy," Flamel said with great solemnity, "the details of which are currently known only to Dumbledore, but which says that you are the one with the power to defeat Voldemort."
"M-me?" Harry squeaked.
"Yes, but that was not the plan for this year. Your encounter in the dungeons was, as far as I can tell, Dumbledore's ill-conceived attempt at training you." Harry got a shocked and horrified look on his face. "I quite agree," Flamel acknowledged him. "He wanted you to face Voldemort in a controlled environment, one where he could step in and help you if need be, but it backfired. Fighting Quirrell to keep the false Stone away from him nearly killed you. When I confronted Dumbledore, he claimed he wanted to help you train whilst still letting you have a normal childhood. Instead, he nearly ended it."
Harry blinked in disbelief. People joked about Dumbledore being mad all the time, but it looked like he really was. That was about the most insane plan he'd ever heard, and after this past year, that was saying a lot. He glanced around the Hospital Wing and noticed something else: "Where is Professor Dumbledore?"
Flamel smiled again and said, "I decided that young man needed a time out."
48 Hours Earlier
Albus Dumbledore finished his paperwork and rose from his desk. It was time he checked on Harry again. He walked to his office door, as usual, and opened it.
And came out in his bedroom.
He looked back through was should have been the door to his closet. He was indeed looking into his office. He stuck his arm back through the door frame and waved it, but nothing seemed amiss about the door itself. He walked through his apartments the long way until he came back to his office and looked through the door that ought to lead to the rest of the castle.
He was still looking into his bedroom.
A quick check revealed that every door and window he could reach led back around to another one in his apartments. The Floo was sealed outright. Albus Dumbledore thought he had seen it all, but this was a trick he had never encountered before. And he had no idea how to get out.
"Fawkes?" he said tentatively.
The phoenix squawked at him indignantly and flamed out of sight. Fawkes hadn't been too keen on his plan for Harry either.
Dumbledore walked through the door to his bedroom again and saw something he hadn't noticed before. There was a basket of unleavened bread on his bed, and there were three changes of clothes laid out for him—all of them robes of coarse, black goat's hair of the kind traditionally worn for penance in the middle ages.
Clearly, Nicolas was more angry than he'd thought—and less forthcoming with his lore than he had always believed.
"I'll let him out as soon as you get out of here," Flamel told Harry, to the boy's amusement. "It's only fair that he suffer the same sentence you have."
"So what happens now?" Harry asked.
"Well, officially, the Philosopher's Stone has been destroyed to keep it out of the wrong hands, and Perenelle and I are setting our affairs in order."
Harry had heard enough spy movies from his cupboard to guess where this was going. "And unofficially?" he ventured.
"Unofficially, Perenelle and I can be anyone we wish. We can disappear from the world, but we won't be far. I am going to train you, Harry—properly—just as I trained Dumbledore to defeat Gellert Grindelwald. It will have to be in secret, though. Baba Yaga will have my head if I interfere in the affairs of mortals openly."
Harry had only a vague idea of what that meant, but it didn't sound good. "How, then?"
"Well, that is where Polyjuice is such a useful tool. While you were asleep, I tracked down a young man who has been misusing magic to his own ends, to great harm to others, and I took the liberty of relieving him of his identity and his rather impressive hair. This summer, that man will suddenly decide to retire from his life of adventuring to become your new Defence Against the Dark Arts professor—Professor Gilderoy Lockhart."