Nicholas Flamel is the Alchemyst. Yep, the book's named after the dude, so we're thinking he's got a pretty big role to play. At first, things seem pretty simple: Flamel is a mentor and guide to the twins, and an enemy of the ruthless Dr. John Dee.
But the more we learn about Flamel, the more we discover he's a pretty complicated guy. For one thing, he has a crazy long back-story. He was the most famous alchemyst of all time, sought after by kings and princes, and has lived for hundreds of years. In the novel, he is best known as the guardian of the Codex, the book of Abraham the Mage. In terms of the effect on Sophie's and Josh's lives, that's what really matters.
They might not be besties, but Dr. John Dee and Nicholas Flamel's destinies are intertwined, and there's no way around that fact. Flamel was once Dee's teacher, and Dee was once Flamel's apprentice and student. Since they're both immortals, but fighting on the opposite teams, we know that they'll be seeing a lot of each other in the books to come, so it might behoove us to make a comparison or two.
The two immortals have different strengths and weaknesses, and those qualities have determined their abilities. Dr. John Dee says that the very traits that made Flamel "such a brilliant alchemyst—his attention to detail, his knowledge of ancient languages, and infinite patience—made him a poor sorcerer and terrible necromancer. He simply lacked the imaginative spark of pure visualization that was needed" (6.6). So, according to Dee, our Flamel is a very smart guy, but not exactly the most creative.
On the other hand, Dee "was probably the finest student... [Flamel] ever had" (5.56), but his greed and jealousy, as well as unbridled lust for power and knowledge have limited his abilities. As Flamel says, "Dee's search for knowledge was always his greatest strength […] and his weakness" (5.29). Here's the thing: what Flamel thinks of Dee probably tells us a bit more about Flamel than it does about Dee. Flamel is clearly a guy who values honesty, loyalty, and good sense. His distaste for Dee's ambition shows that Flamel thinks there are more important things than power, which sounds pretty humble, coming from a guy who can live forever. Or at least as long as he's got that book around.
But to be honest, it's also a little ironic that Flamel calls Dee out on his unquenchable thirst for knowledge, because one might say the same thing about the Alchemyst. After all, isn't Nicholas Flamel's yearning for the knowledge of the Codex the reason the entire world might be destroyed? Even Flamel acknowledges his search for knowledge might have gone too far:
In recent years, Nicholas would sometimes awaken at the quietest hour of night with a single thought spinning round and round in his head: if he had known then what he knew now about the Codex, would he have continued his research into the philosopher's stone? […] Most nights he answered yes: even knowing all he knew now, he would still have continued his studies and become the Alchemyst. But there were rare occasions, like today, when the answer was no [… there was] a chance that he had doomed the world. (18.20)
If he's being honest with himself, Flamel might just have to cop to the fact that the whole reason they're in this mess in the first place is that he had to be all nosy and find the secret to immortality. But that's also the gift of hindsight talking. Who could resist immortality in the moment? Especially if you haven't really considered the possible fallout.
Flamel is a scientist. By nature, he's driven to explore new knowledge. But the pickle he finds himself in in this novel shows us that knowledge without consideration is, generally, a very bad idea. Think before you do, Flamel says. Or you'll pay the price some day.
No matter what has happened in the past, Flamel can only really deal with what's in front of him. He's here to regain the book, protect the twins of the prophecy, and train them to use their magical powers. Oh, and he's also here to save his wife, Perenelle, fight off ancient Elders and his powerful enemy Dr. John Dee, and… um… save the world. That's a pretty tall order.
Throughout the novel, however, Flamel works his hardest to do all this and more at great personal cost. He convinces Hekate to Awaken Sophie and Josh, recruits Scatty to help protect them, battles for the Shadowrealm, and guides the gang to the Witch of Endor in order to train Sophie in the elementals of air magic.
He faces great physical peril—not just flying darts and razor-clawed cat goddesses, but also the fight against time—as he and his wife age a year for every day they go without the elixir of life contained in the Codex. He's like a hero on an old-fashioned quest, sacrificing himself to save the damsel, defeat the beast, and help whoever he can along the way.