Nicolas Flamel historically existed as a simple scrivener and manuscript-seller, yet the legends directed at him only rose around 1612. Nobody ever really knew he was an alchemist until his secrets circulated about 194 years after his death. The story of Joachim Flamel would fill you in on every detail there was, including how Nicolas had a child to begin with.
Unlike the religious scholars, alchemists of the Middle Ages sought after the philosopher's stone, the legendary substance capable of turning any metal into gold and even turn into the elixir of life. The marriage of Nicolas and his wife Perenelle were arranged by their parents in order to secure an alliance between their families in pursuit of the so-called symbol of perfection in alchemy. Perenelle hailed from a rich lineage, and has brought the wealth from her two previous marriages. In order to fund their constant experiments, they owned several properties and shops. However, they still rendered financial assistance to churches and hostels, and were known for their philanthropy.
Both families were favored by the gods, from whom they received their powers to practice alchemy, tracing way back to the time of their ancestors. During those times, most members of both families defected to start new and ordinary lives; some were even killed by rivaling alchemists. After failing a lot to create the philosopher's stone, they thought there was no point in continuing on. Thus, the remaining kin decided to never practice alchemy again.
Now forbidden to unearth the family's secrets, Nicolas and Perenelle roamed across France in an seemingly endless search of ways to achieve the philosopher's stone, to bring back honor and glory. During their stay at Mont Saint-Michel, they came across a thief of about 12 years of age, who stole a book from a traveling abbess. They were able to return it to her, who revealed herself to be Hecate. Having known about their family history, she offered them the book which she called the Codex. It contained the greatest secrets of alchemy, far more valuable than all resources their families had combined.
However, Hecate had set up a barter in exchange for the Codex. Someone had to be a living testimony to the success Nicolas and Perenelle would achieve, and at the same time someone who would guard both the book and the philosopher's stone should anything happened to the couple. Basically, Hecate wanted a child with Nicolas, with his wife's blessing, of course. Perenelle knew it was for the sake of their work, and was generally okay with the whole idea. She knew better not to go against a goddess. About 6 months after their return to Paris, the child arrived, whom they named Joachim.
Around the same time, the thief, who was an orphan named Benedict, appeared at their shop's doorstep. He seemed to have followed them all the way from Mont Saint-Michel, and begged them to take him in, even as a slave or the like. Seeing how they spared him from the "abbess", he knew they were kindhearted. Nicolas and Perenelle didn't trust him, and just sent him out. Benedict, however, was persistent, as he stayed outside every day. One time, he sneaked around their laboratory, and was caught performing alchemy, much to the couple's surprise. At that point, they took him under their wings and became their apprentice.
Joachim and Benedict were educated by Nicolas and Perenelle at home to avoid their family's secrets from spilling out. They sometimes visited their relatives, remnants of once powerful families, in Bordeaux but never told them about their activities. Even if they would, they would vaguely remember, because the family traditions were either lost, brought to the grave, or burned to ashes. Back at Paris, Nicolas had a stable job at court while Perenelle handled the rest of their businesses and properties.
When Joachim was 7, the Flamel family embarked on a quest across France once again to decode the Codex, and after about 5 years of spending a lot of money and resources, the couple with the help of Joachim and Benedict, were able to create the holy grail of alchemy - the philosopher's stone in 1389. The groundbreaking achievement was kept secret within the family, and they quietly returned to Paris without saying a word. They thought it would be best to hide the stone for the time being, and resumed their normal lives.
One year after, Perenelle was diagnosed with a rare terminal disease which would eventually kill her in a matter of 4 years. Desperate for a cure, Nicolas resorted to the Codex and the philosopher's stone, in which he produced the Elixir of Life in order to prevent his wife's imminent death. Although she was cured and rendered nigh immortal, the elixir's recipe magically changed every month, so Nicolas had to concoct it over and over again to keep Perenelle alive, not to mention the recipe cannot be memorized.
A few years had passed, and rumors of a wealthy family moving into Paris spread throughout. They called themselves the Montmorencies, who were alchemists at the pretense of prophets and miracle-workers. They have moved into the city after getting news of the philosopher's stone being made by the Flamels. They planned to use the stone to create and modify a human being, the process known as human transmutation—a forbidden taboo in alchemy.
Around the same time, Joachim also had his first monster attack after a chimera came bursting through his family's shop. Although he was able to kill it when he awakened to his demigod powers, it left Benedict with one perfectly normal leg. You see, it got bitten off before Joachim came to the rescue. Ever since then, Nicolas created a metal leg for him. This part wasn't really relevant, but whatever; it's for the sake of stating a monster attack.
Now, let's cut to the chase. You see, Benedict worked as a spy for the Montmorencies all along, and has waited a long time to steal not only the philosopher's stone but also the Codex which contained the recipe needed for human transmutation. Now an accomplished alchemist, he replicated the Codex and stone to fool Nicolas before leaving. It was too late when the latter found out that they were missing, and the elixir's effects wore off. Sadly, Perenelle died because of this, at the year 1397.
The death of Perenelle drove Nicolas to desperation, while Joachim was determined to avenge her. With his broken father in tow, he boldly went to the villa of the Montmorency family to negotiate with the head, Alphonse, who was a very powerful sorcerer. Seeing how hopeless Nicolas was, he easily convinced him on using human transmutation to bring back his dead wife. For the sake of his father, Joachim went along with Alphonse despite his absolute defiance against his plans.
During the attempt to bring Perenelle back to life, Joachim sabotaged the whole experiment which ended in a terrible disaster. Many lives were killed by the numerous explosions of magical substances, including that of Alphonse's and Benedict's. Joachim, on the other hand, lost his right eye and leg (the same as Benedict, yes). During the ensuing catastrophe, Nicolas carried off his son along with the stolen Codex and philosopher's stone. The alchemist quickly created the elixir of life once again and gave it Joachim, wherein he was saved from a menacing exsanguination. After he made sure he was safe from death, he transmuted a glass eye and metal leg to replace the missing parts.
It wasn't before long when the remaining Montmorency members pursued after them. Nicolas decided that he should surrender in order to stall for time while Joachim took the Codex and the philosopher's stone with him and fled Paris. Hecate's words came true at last, which Nicolas only remembered at that point. Kissing his father goodbye, he escaped just as he saw him being dragged away in chains.
Armed with newly-discovered magic powers and alchemy, he made his way for his relatives in Bordeaux, while fighting monsters along the way. He was almost restless the whole trip, fearing that the Montmorencies would catch up to him. However, he soon ended up lost, and found himself trekking across sandy beaches of Normandy and into Mont Saint-Michel. There he met Hecate, disguised as the same abbess as before. She told him about the Greek gods, and the reason why he was born. With everything settled down, she told him to stay on the island with the Benedictine monks, some of whom were magicians and alchemists like him. It was the safest place for him, and for the treasures he held. In the following years, he lived in the abbey, secretly trained by the monks in the art of magic and sorcery. In 1418, Nicolas Flamel died at the age of 88, having continued his work after escaping the Montmorencies for the second time.
Joachim took off from Mont Saint-Michel after it was besieged twice during the Hundred Years' War. From there he traveled across France, and then throughout Europe, and then throughout the world. In 1612, he spread the story of Nicolas and Perenelle Flamel in their pursuit of the philosopher's stone. From there, the first book published attributed to them was the Livre des figures hiéroglyphiques or Exposition of the Hieroglyphical Figures. Soon, more and more legends about them arose, and the world knew them as they were until today.
I wouldn't bore you with the following centuries, but it was sufficed to say that he entered a lot of jobs and professions as he spent his time on the world: a swashbuckler in the Spanish Armada, a bartender in a Finnish tavern, a bookseller in a Venetian bookshop, a cook in a Mexican pueblo, a herbalist in a Venezuelan market, a shepherd in Israelite pastures, a street sweeper in Saudi Arabia, and a lot more not listed. It wasn't until 1922 when he decided to come back to Mont Saint-Michel and lived a peaceful life with the monks. If you're going to ask why he was still alive at this point, you've probably forgotten about the Codex and the philosopher's stone by now. That time around, he has made countless copies of the two objects, in case anybody wanted to steal them.
Unfortunately, his 92-year stay on the island was ended when the descendants of the Montmorencies suddenly arrived. The family was supposedly extinct over the course of the centuries, but a man named Ignatius Montmorency stood up and took the burden of continuing his ancestors' mission of stealing the philosopher's stone, this time to resurrect Alphonse himself. He was a very formidable man, as he nearly killed Joachim in a magical duel. With a burst of putrid smoke, he used the last ounce of his energy and fled for New York, where he ended up at Camp Half-Blood, and was finally claimed by his mother Hecate.