An aura stone is an item featured in Professor Layton and the Azran Legacy. There are five of them scattered around the world, and were left by the Azran Civilization before they were wiped out. The Azran Dome in Kodh reveals the locations of these "eggs", all located in Phong Gi, San Grio, Torrido, Hoogland, and Mosinnia. Professor Layton and the group travel in the Bostonius to these locations to collect all the eggs, with Targent constantly hot on their heels. When combined, the aura stones form a key, allowing the holder of the key to access the Azran Sanctuary, and the secrets of the Azran.
The aura stone located in Phong Gi is found almost instantly upon the group's arrival; around the neck of the town's chief, Morel. For one to obtain it, they must make the chief laugh. This proved to be difficult for not only Layton and the others, but for the villagers as well, as a man once the life of the party had not been laughing for weeks.
Layton and Luke attempted to make Morel laugh by wearing masks, and Professor Sycamore had told him one of his jokes, but to no avail. They seek out information around the town why the chief had not been laughing lately, and Layton soon discovers that he is going blind. The group gather up local resources in order to make the chief a pair of glasses. After putting them on, Morel begins to laugh non-stop, and in keeping his promise, gives his aura stone to Layton.
Finding the aura stone in San Grio proved to be difficult for Professor Layton and the others, as the town was filled with items that looked like the aura stones, named "popoños". They seek out information as to the whereabouts of the real aura stone, and one of the residents, Bud, reveals to them that the true popoño was used in a tradition created by the town, in that the true popoño is passed around to bring happiness. This aura stone was found several years ago by Eduardo Popoño during a low time in his life, and the egg had brought him great joy. He started the popoño-passing tradition in order to spread happiness to those around him. Bud then reveals that if the group wanted information about the true popoño's whereabouts, they would only have to mention the word "harmony", however no one was able to reveal names as to who had the popoño.
Layton and the other set about asking several residents around town for information on the aura stone, and discovered that one of two rules applied as to who received the true popoño; one must pass it to someone of opposite gender, or of opposite marital status. With these rules in mind, they discover that Bud had the aura stone all along, and he had hoped they would come back to him for it. He gives the aura stone to Aurora, who he felt could do with some happiness.
The aura stone found in Torrido is found upon arrival of Professor Layton and the others. It is seen around the neck of a dangerous looking wolf, Old Red. They seek out information about this creature, and discover that he often comes down from an abandoned mine outside of town to terrorize the townspeople. With information courtesy of the town's sheriff Flint, they visit the abandoned mine in which Old Red resides, and find two Targent agents about to shoot the beast, but to Old Red's luck, the gun wasn't loaded and they make their escape. Luke uses his power of talking to animals to find out why Old Red often visited the town, and reveals that he had been looking for someone with black hair and pigtails, as he felt his life was drawing to an end. He wished to thank the girl for saving his life before his life ended.
In an attempt to grant the beast's wish, they go searching for a girl of this description, and they find a young girl named Scarlett that fit the description perfectly. They bring her to Old Red, but he tells Luke she wasn't the girl he was looking for. Confused, they decide to ask Scarlett's grandmother Ruby who could possibly fit the description, but before they could find her, Layton sees a picture of a young Ruby, and suddenly realizes that the girl Old Red had described was Ruby herself, as she had saved him many years ago. After finding Ruby, they take her to the abandoned mine to see Old Red, and he wished to give back the aura stone she had given him as a sign of their friendship. She reluctantly took the chain off, and suddenly Old Red's sickness had gone away, as the tight chain was the cause of his apparent sickness. Knowing they weren't in Torrido only to help Old Red, Ruby gives the group the aura stone as a thanks.
Upon arriving in Hoogland, Aurora senses a strong presence of an aura stone in the area, but before they begin searching for it, they are notified of a wedding happening in town. Emmy was eager to take pictures of this wedding, so they ask around where it would be. They follow the bride to the chapel on top of the hill, to see the ceremony ending after she had been locked inside, after she was seen arguing with a man. This would be known as a disturbing tradition of Hoogland, in where brides were sacrificed to the mythical Dragonlord so that they would continue to be brought fair winds. The brides were locked inside the chapel, where they would turn to wind. The town's tradition infuriates Emmy, however their attempts to free the bride achieved nothing. One of the residents, Beatrix, reveals to the group that she had aided in freeing the brides who had become victim to this tradition, allowing them to escape to another town. The brides sacrificed themselves willingly in a bid to escape Hoogland. However the bride currently in the chapel, Romilda, was reluctant to leave, and felt that only her fiancé, Julien, would convince her to leave. She then informs them of a secret way through the forest to get to the secret passageway of the chapel.
The group set off to convince Julien to accompany them to the chapel, and he was determined to save his lost love. They traverse through the forest to find the secret passage, and find Romilda still inside. She still wasn't convinced in leaving, as she wanted to prove of how fake Hoogland's tradition was. Eventually, Layton notices one of the aura stones at the Dragonlord's altar, and solves the puzzle in this ancient Azran site to bring balance back to the winds of the town. Eventually Romilda is set free, and Layton and the others take the aura stone with them.
Professor Layton and the others arrive to deserted streets in Mosinnia, and a young boy by the name of Umid requests their help in awakening the sleeping adults in the town, who had been in a non-stop slumber for the past week. He tells them of a legend in the town, in that tears from a phoenix would cure any sickness, and wishes to seek out this phoenix. They seek out information from the children in town, and a young girl, Mehri, tells them that the town elder, Dana, had been speaking of a phoenix in her sleep, and so they listen to what she had to say at the temple. They then solve a series of puzzles that seemed to be of Azran origin, and eventually they are led to the sluice gate outside of town.
They open this gate, and the water flows into the canals, revealing that the canals in the town took shape of a phoenix. Taking the legend into account, they locate a hill that represents a phoenix eye, and discover that inside the hill was an ancient Azran library, which reveals the cure to awaken the adults. After the adults had awoken, Umid's mother, Banu, reveals that the adults had eaten a special type of mushroom that put them to sleep, unaware of its presence at the festival. As a thanks, the town elder gives an aura stone to Aurora, believing she was the guardian spoken of in the legend.
After obtaining all the aura stones from the five locations, Professor Layton and the others discover one of the eggs is a fake, all thanks to Targent. They discover the last egg is located in a place called The Nest, which turns out to be Targent's headquarters. Upon arrival, they notice an injured Mackintosh, and follows him to one of the airships. They save him, and take him back to the Bostonius in Raymond's care. Upon leaving the Bostonius, they see Macaw and Robin, the two Targent agents that had followed them around the world, deciding they wanted to quit Targent. Since they were to make an escape, Layton asks them to take Mackintosh with them so he could get proper medical attention.
The group then make their way to the Obsidian Tower, where Bronev was waiting for them. After scaling the floors of the tower, they make their way to the top, and Swift lets them into Bronev's office. Upon meeting with him face to face, Bronev instantly offers for Layton to join Targent, but he naturally declines. He then offered they play a game, to see who would take possession of the last aura stone, and after Layton wins, Bronev then threatens his parents if he chose not to join Targent. He soon leaves, and after taking the five aura stones, Aurora uses her power to combine them into one large key. Afterwards, she remembers everything about the Azran, and if they unlocked their secrets, they would be in grave danger. Professor Sycamore offers to take care of the key, and instantly reveals himself to be Jean Descole, who had strung Layton along on his pursuit for the eggs for his own gain.