After working at the crystal shop for a month, Santiago suggests that the shop owner build a display case for the crystal to attract new customers. The owner seems resistant to change, as if he is afraid of success. The owner then tells Santiago that, although he has always dreamed of making the pilgrimage to Mecca, he knows he will never do it. He tells Santiago that he is afraid that, once he achieves his dream, he will have no need to go on living. Santiago ends up convincing him on certain issues, and within the year Santiago spends working at the shop, the owner makes several changes that improve business. At the end of the year Santiago resolves to take the money he has saved, buy a flock of sheep and return to Spain. As he takes his leave, he asks the shopkeeper for his blessing; the shopkeeper gives it, but tells Santiago that he knows he will not return to Spain. The shopkeeper reiterates that he himself will likewise never go to Mecca. He claims that this is maktub - or written by God. Santiago realizes that while he is far from home, he is actually closer than ever to the Pyramids and the treasure. He resolves to take a chance and join a caravan across the desert in search of his treasure.
When Santiago goes to the stable to take the caravan, he meets an Englishman, who is in search of a famous alchemist living in Al-Fayoum oasis. The Englishman is obsessed with finding the common language of all the world and has spent the majority of his inheritance traveling and studying science, religion, and finally, alchemy.
While Santiago and the Englishman are waiting for the caravan to leave, Santiago takes out Urim and Thummim and the Englishman immediately recognizes them. He carries the same two stones in his own pocket. He goes on to tell Santiago that it is not accidental that the two of them met on the caravan. Coincidences and omens are the universal language that the whole world can understand. It is the task of alchemy to decipher this language. Santiago realizes that the series of events which led him to this point - meeting Melchizedek getting robbed and happening upon the shopkeeper and the crystal shop - where not accidental or random at all but were signs that he is nearing his Personal Legend.
The caravan begins to move across the desert, and Santiago learns many things from the English alchemist and the guides of the caravan. The desert is enormous and dangerous, and the guides teach Santiago about listening to its language of omens. The Englishman refers to the Soul of the Word and describes it as the principle that governs all things. When we have an intuition or truly want something, we are immersed in the Soul of the World. This is not a strictly human gift, though; everything on the face of the earth has a soul and a Personal Legend. Santiago is interested and asks to borrow the Englishman's books about alchemy.
Reading the Englishman's books, Santiago learns more about alchemy. He finds out that the goal of alchemy is the Master Work. The Master Work is part liquid and part solid; the liquid is called the Elixir of Life and the solid is called the Philosopher's Stone. The Englishman's books tell the stories of all the famous alchemists who dedicated their lives to realizing their Personal Legends. As he reads on, Santiago realizes that he and the English alchemist are pursuing the same thing, but Santiago prefers to read the omens of the world in his everyday life instead of in old musty books.
While the caravan moves across the desert, there is a war brewing amongst the tribes of the region. It is becoming more and more dangerous by the day, but the caravan has no choice but to carry on and hope for the best. From the stoic guides of the caravan, Santiago learns the value of concentrating on the present.
Part II of The Alchemist shows Santiago encountering two more setbacks before he can reach his destination. Part of the artistry of Coelho's narrative lies in the way Santiago's setbacks, or complications, become progressively more and more complicated. While the first setback - getting robbed in Tangiers - is admittedly serious, it is also relatively prosaic. Looking ahead, the second setback, Santiago's love for Fatima, is more complicated because love is not usually presented as a setback. Santiago, however, contemplates suspending his quest, something not even being robbed in a foreign land could do, to stay with Fatima. The reader sees, once again, Santiago pondering his options and relying, once again, on outside intervention to make his decision. Even though Fatima tells Santiago that she wants him to continue, he is still undecided. At this point, fate intervenes both in the form of the omen in the desert and the alchemist telling Santiago his future of resentment and regret if he doesn't pursue his dream. As a result, once again, Santiago continues.
The final complication, Santiago's feat of turning himself into the wind, is different in a few ways. First of all, it is by far the most profound. Whereas the first two were essentially physical and personal setbacks, the last one is spiritual in nature. Santiago comes to realize that he and God are one soul and that his soul is a small part of the greater Soul of the World. Secondly, the last complication is different in that Santiago overcomes it entirely by himself. There is no intervention on the part of the Alchemist or anyone else. This is in keeping with the dual-narrative modality at play in The Alchemist - a physical narrative and arc paralleled by a spiritual equivalent. The scene wherein Santiago turns himself into the wind is the climax of the spiritual journey, just as the discovery of the treasure is the climax of the physical journey.
By working at the crystal shop, Santiago learns many lessons. One of the most important is that it does not take an exterior force to prevent one from realizing one's dreams. The shopkeeper is actively trying to avoid achieving his dream, because he believes that if he achieves it he will have nothing to aspire to. It is with this in mind that Santiago decides to continue on his own quest.
The theme of fate is touched upon again in the meeting of the Englishman and Santiago. In many ways, these two form two sides of the same character - the seeker of knowledge. In many ways, they are both seeking a treasure: the Englishman wants to learn how to turn lead into gold and Santiago is seeking a buried treasure. Both of them, however, realize that there is much more at stake than just material wealth. They are different in that the Englishman insists on learning everything from books. These books form the basis of all of his knowledge, so much so that the real world is secondary. Santiago, on the other hand, is constantly learning by observing the world, the desert, the omens of life. The characters are, however, intimately joined by fate.