Amy also invented a word "Azturpealean" in the book "Storm Warning", because she couldn't think of a color to describe the ocean water.
What would happen if you discovered that your family was one of the most powerful in human history? What if you were told that the source of the family's power was hidden around the world, in the form of 39 Clues? What if you were given a choice – take one million dollars and walk away…or get the first clue? If you're Amy & Dan Cahill, you take the Clue – and begin a very dangerous race.
Amy, Dan, and their au pair, Nellie, found music by Wolfgang Amadeus Mozart so they go to Vienna, Austria, to learn about him. On the train, Holts attack them to steal the music, but they fail. In Vienna, Amy and Dan discover that Mozart had a younger sister: Maria Anna "Nannerl" Mozart. They go to a library and ask for her diary but find out that Jonah Wizard stole it. They steal it from him, then Nellie translates it and notices that three pages are missing.
Then, Amy and Dan discover that there is another song in the middle of the song by Mozart. That song's name is "The Place Where I Born", so they go to the place where Mozart was born: Salzburg, Austria. There, they see Alistair Oh, and follow him. He goes into the Salzburg Catacombs, and they go in there too. There, Amy and Dan see The Man in Black, and there is an explosion, but they escape.
In Venice, they follow Jonah Wizard, and find a secret passage from a music store called Disco Volante to a Janus stronghold. There, they find the missing diary pages, and steal them. The pages say that Nannerl Mozart thought her brother was going crazy because he was getting into debt by buying Japanese steel. A name, Fidelio Racco, which was also found on the paper taken from Alistair Oh, appears in the diary. Because of that, Amy and Dan go into Fidelio's Racco's mansion (which is now a museum). There they see the Kabras, who attack them, but fall into a booby trap, and are knocked unconscious.
The book starts with Dan and Amy in a Venice airport. There, Ian and Natalie Kabra steal their plane tickets and board a plane where their, Nellie who is already on the plane. Then, Amy and Dan are then forced to team up with Alistair Oh and fly with him on his private plane to Japan. Together they learn about Toyotomi Hideyoshi, the greatest warrior in the history of Japan, and the son of the first Tomas.
While Amy, Dan, and Alistair are researching, the Holts take them captive, forcing them to lead the Holts to the possible site of a clue—a Tokyo subway station. When a train approaches, the Holts run. Amy's foot gets stuck in the tracks, and Dan struggles to pull her out. Before the train hits them, Alistair pulls them out of the way into a hidden room. Amy is saved but suffers a sprained ankle.
In the room, they find a haiku, which tells them to use geometry to find Hideyoshi's treasure. Later, they find some geometric shapes, but are chased by the Yakuza, who throw shurikens at them. They are rescued by Nellie, who has struck a deal with, and is accompanied by, the Kabras. When the Kabras give Amy and Dan a small coin of importance to the search, the two Cahills agree to join forces with the Kabras. They decode another message in the shapes, and some English letters. The message tells them to go to Korea.
In Korea, everyone goes to Alistair's home. There, they look at old books about the Cahill family in Alistair's secret library. By reading one of them, Amy and Dan figure out that the secret of the 39 clues is the ability to make gold out of lead. They also figure out that they should go to a mountain called Pukhansan.
In the mountain, they find an entrance, and open it with the coin they have. Inside, they find all of Hideyoshi's treasure, and the third clue, gold. The Kabras then betray them and block them inside the cave. Dan and Amy make it out but Alistair appears to be crushed under falling rocks. They also see Bae Oh talking about this with The Man in Black. Upon returning to Alistair's estate, Dan sees Alistair's gloves (which he was wearing before the cave in), and realizes that he isn't dead. They also figure out that the next clue is in Egypt.
Dan and Amy learn about female pharaohs and goddesses like Isis. They discover how the Clues corrupt even the most brilliant Cahills and question Grace's love for them when they discover a secret Ekaterina stronghold at a Cairo hotel that they were staying in, the Hotel Excelsior. Later they learn that the hotel is owned by Bae Oh, the head of Ekaterina. Along the way, Grace's best friend, Hilary Vale, gives Amy and Dan several items from Grace. They discover that Grace is helping them find the next Clue. Amy and Dan work together with Alistair at the end of the book to reach the original location of the Clue, which is underwater. But they learn that the Clue has been stolen by the Madrigals. Alistair leaves Amy and Dan to look at books at his library. Then Amy and Dan realize that Grace didn't want them to go to the original location of the Clue, but to a store in Cairo. There, they receive a picture of a leaf of a plant. Then they go back to the Hotel Excelsoir, the hotel which is the location of the Ekaterina stronghold. There, they discover what the Clue is. A half gram of Myrrh. The book ends with Amy and Dan discovering that the Ekaterina stronghold has been destroyed by the Madrigals, and the place where Amy and Dan are headed next is not revealed.
Amy and Dan Cahill getting a telegram in Egypt. Fearing their lives, they had changed hotels in the night. The telegram told them to go to a locker in the airport, but to come alone. They leave Nellie Gomez a note and leave. They are closely followed by Hamilton Holt. In the airport, they lose him, but then run into the Kabras. Dan makes a run for it but Ian grabs Amy quickly. She then kicks him in the leg extremely hard. They make it to the locker in time to discover objects in a box left by a mysterious person who goes by the name of NRR. In the box there is a guidebook, disguises, passports, a snow globe, a credit card, a note with random letters on it, and a photo of their parents outside the Russian Embassy. Dan and Amy unscramble the random letters and find out that the next clue(s) is in the following Russian cities: Volgograd, Moscow,Yekaterinburg, and St. Petersburg. They board their plane quickly without Nellie or Saladin. Then they both fly to Russia, ending up in Volgograd. Here they meet and work with the Holts, climbing the inside of The Motherland Calls to discover a hint to the clue around Rasputin, Anastasia, and Alexei. They check out the cities on the list they found by the eye of the statue, leading them to the place Rasputin died. During an attack by the Kabras, the Holts alert them of a location code which guides them to a Lucian base. There, they discover who the mysterious NRR is; Nataliya Ruslanovna Radova, Anastasia's only daughter. They also find the clue in the Amber Room, located by Nataliya. The clue was one gram of melted amber.
Amy, Dan Cahill and their au-pair Nellie Gomez head to Australia to discover what their mother and father knew about the clue hunt. But following her parents' footsteps reminds Amy of the memories she had of the night her parents died...memories so painful she can't even bear to share them with Dan. Amy and Dan have to decide how much they're willing to risk, and what they are fighting for. Isabel Kabra joins the hunt, as she could not stand the mistakes of her children. They cannot decide which Lucian to trust - the cloying Isabel Kabra, or the serious but deadly Irina Spasky. Their terrible blindness in seeking the wrong ally leads to the death of a hidden ally - Irina. Irina stops following Isabel and helps Amy with the clue hunt. She turned away from Isabel because she lost her boy, Nikolai, when Isabel forced her to accomplish a mission (and believes that it is Isabel's fault). At the end Irina Spasky chooses to save Amy, Dan and Alistair at the price of her own life. The clue was water.
Shocked by the death of Irina Spasky, Dan and Amy march into danger once again. For the first they begin to question how much they trust their au pair, Nellie, later they regain their trust. The storyline starts the morning after the fire that killed Irina Spasky. The two were shaken by whats' happened and they can't believe that Irina was on their side after all. But moment later, Nellie Gomez, their au pair, appeared signaling the arrival of police. It turns out that Isabel Kabra called the police and put the blame of Irina towards Alistair.
Meanwhile, after using again their code breaking abilities, Dan and Amy figured that the last words of Irina was actually a song. "I'm with you and you're with me and so we are all together" which points to their next destination: Pretoria, South Africa.
Upon arrival in South Africa, a mysterious man hands a postcard to the sibling which points to a connection to a famous person called Shaka. As they unravel the history of Shaka, they find out that he was a member of the Tomas branch. Following a line of clues, Shaka was then connected to Winston Churchill.
While visiting a library with a document coming from Churchill, they discover that the clue was hidden with the body of Shaka. They also find a tunnel in which it is said that Churchill hid when he was in Africa. They unlocked the message of the Churchill which pointed to a certain coordinate which turned out to be a Tomas Stronghold.After infiltrating the Tomas stronghold they soon discovered a box with diamond in it. At first they thought that was the clue, but Aloe turns out to be the clue (which was growing around the box)
When they were leaving South Africa, they were captured by the Kabras. They were about to kill Dan when suddenly the professor (which helped them at the Tomas Stronghold) saves them again. They escaped together with what Dan thought was the vial with green liquid that they thought was the lead to their second clue in the Maze of Bones.
They escape them by flying Grace Cahill's old plane. During the ride, Dan and Amy have a little quarrel, accidentally breaking the vial and some of the contents spill onto Dan's arm. It turns out to be a Kabra poison. To get the antidote, they fly towards Grace Cahill's home in Madagascar. In Grace's journal, they find a page that says ″I am feeling melancholy today, thinking about my dear A & H and missing them so. I cannot even bear to listen to my beloved di Lasso, because of the reminder...″ and on another page it says ″I have written Deng Xiaoping, who has agreed to grant to visit to A & H when he discovered that they, like him, are M (Madrigals)."