Dan was only four when his parents, Hope Cahill, and Arthur Trent died in a fire, he and his sister Amy got out of the building. He then was sent to live with Beatrice Cahill, but not in the same house as her, but with an au pair in an apartment. On the weekends, Dan went to Grace Cahill's house, his grandmother. He once broke into her display case and took out an Aztec dagger, and Grace told him about it. While Grace and Amy had picnics, Dan would explore the tombstones. He liked to get grave rubbings and posted them in his room. In fourth grade he won first place in the science fair with a model volcano, then got detention for hiding it in the principles sidecar, and for wearing his ninja costume to English class. In 5th grade he got a school record on a state math test, and in 6th grade got detention for gluing the teachers desk to the ceiling during recess. Dan liked Nellie Gomez, his most recent au pair, who made great waffles, let him almost set the next building on fire, and didn't her when his bottle rocket collection went off, hitting the building across the ally. Dan also went to the week-long winter holiday at the Cahill manor. Dan goes to Adams Middle School and once arranged a fake mascot head exhibition so he could take them for his collection, and was banned by Nellie from using cutlery as swords so posted a Want article on Crazee Collectors for swords or katana.
When Grace died, Beatrice drove them to the funeral, denying Dan permission to wear his ninja costume. On the drive their he argued for Nellie's stay as their au pair. At the funeral, Dan was held upside down by Reagan and Madison Holt, while Hamilton, their older brother, taunted Dan that Grace would give him the estate. Amy tried to held, put got nervous. Dan then noticed Ian and Natalie Kabra. At the funeral, Dan put a shovel of dirt on Grace's grave, and then he and Amy were invited to the will reading. William McIntyre played a video of Grace explaining the Cahill family heritage, and that you could take a million dollars, or hunt for the 39 Clues. Dan instantly decided to take the money, but after a while Amy was able to ease him into taking the hunt. They were the last people to decide, and they did so at the risk of Beatrice disowning them. After they took the hunt, they got the clue card saying RESOLUTION. Fine print. Seek Richard S____. When everyone else left, William talked to Amy and Dan about Grace and warned to beware the Madrigals. He gave them a tip to do what they do when they need to find stuff, and Amy rushed to library, Dan in tow.
At the library, Amy found nothing by a Richard S until Alistair Oh arrived telling her they had to be books elsewhere. Dan found the Cahill crest, and pressed the letters of the branches and a secret staircase was revealed going into a secret library. Alistair found a folio from 1500, and Dan suggested selling it on eBay, but was shot down. After seeing a push-pin map of Cahills, Amy rushed to the Fs finding Poor Richard's Almanack by Richard Saunders, or Benjamin Franklin. She then found her mom's handwriting saying to follow Franklin. Alistair inspected it and found writing by Grace, his father, and Grace's father. Amy found Saladin and Grace's jewelry box when smoke drifted in. Amy and Dan took off up the stairs to find the door blocked. They ran back down and crawled Dan saving Saladin. They followed dragons on the carpet to a duct that Dan and Amy climbed up, and out to Grace's grave. Behind them the mansion was in flames, and Amy saw Mr. McIntyre on the ground, passed out. As she was going to help him, Dan tackled her, pointing out The Man in Black. After he was gone, Amy and Dan ran to William, found his phone and dialed 911.
The police detectives told them it was probably arson and Dan mentioned Alistair. He then was put in the back of a police car with Amy and Saladin. Amy told him they needed a chaperone and when they were dropped off, they realized Nellie would be perfect. They came in and Dan saw Nellie ate his ice cream, and they woke her, Amy telling her they were going on a family 'scavenger hunt' worldwide, and they'd pay for it by selling Grace's jewelry. Even though her father disagreed, Nellie accepted anyway. Dan packed his suitcase with his only photograph of his parents, and told Amy he'll sell his collection.
Nellie booked a train into Philadelphia as Amy realized that follow Franklin meant he ran from Boston. So they got there, and at the car place, Nellie gave them a package waiting for them from Mr.McIntyre. Amy opened it and saw a light and if they found the information meet him at Independence Hall. They drove on I-95, Amy seeing NedTed, and Sinead Starling tailing them, so Nellie sped through three lanes of traffic off an exit ramp. They stopped at the Philadelphia Library Company building, and Amy looked a documents of Franklin, while Dan used the internet to realize Mr.McIntyre had given them a black light reader. The librarian said that Franklin's letters there didn't have secret messages, but maybe the ones at the Franklin Hall did.
After reaching the Franklin Hall, they began to look around when Amy spotted the Man in Black. Quickly they ran to the area with his letters, and Dan began running everything under the black light, until he found a note saying that Franklin's leaving because of something that broke up his kin. Then Sinead Starling took a photo of it on her camera phone, and told Amy and Dan to give the Starlings a head start or Ned and Ted would find out. As they backed out Amy tried to warn them of the Man in Black, but they didn't care and walked through the archway, and there was a massive explosion and the Starlings were crushed. Amy grabbed Sinead's phone and they went to Nellie who was furious, saying she'd call Beatrice. Nellie drove them to Independence Hall where they met with Mr.McIntyre who said the Starlings survived, and that teams were targeting Amy and Dan. He told them Jonah Wizard had booked an overseas flight, and Amy realized they needed to go Pairs. Amy then gave Saladin to Mr.McIntyre.
When they got back, Nellie said they should go to Social Services as she got a voice mail. Amy pleaded that Nellie would take them to Pairs because its important to the family. Nellie agreed, and they flew to Pairs, Dan spilling pasta on Amy, and Amy reading a Franklin biography and two Pairs guidebooks. At the airport they saw Jonah Wizard with the paparazzi. Jonah and his dad, Broderick, saw the three, and they got in his limo. Jonah talked about his merchandise and compared himself to Franklin, Amy got angry and said they wore lockets with his picture, dressed like him, and put his face on chamber pots. The last one got Jonah and his dad set up chamber pots. Jonah asked them to help him track down clue information, but they refused and got out of the limo. Amy then saw Irina with the Almanack, and they began to chase her down. It was easy following Irina, even through the Métro stations, and she reached the Institut De Diplomatie Internationale, a Lucian stronghold. Dan saw Irina's code in, 5910, and Amy and he slipped inside.
No alarms sounded, and there weren't any Lucians, causing Dan to go to library and take a Franklin Battery and a concussive grenade. They found Irina at the computer table bringing up 23 Rue de Jardnis, on the Île Saint-Louis. They wen down after Irina left, and were attacked by guards, but they still managed to slip through the Lucian defenses and out of the stronghold. Dan realized how fun that was, and he and Amy got some bread at a bakery. They walked to the isle, and reached #23, a graveyard. They saw a grave with their names, and the ground collapsed, Amy and Dan falling in. The Holt family formed up around the pit, Eisenhower asking if they found the Maze of Bones and that they'd read the Almanack, Hamilton that they were behind the mansion fire and the museum bomb. A cement truck pulled up with thugs to bury Amy and Dan, but Dan lied Amy knew the clue, so Eisenhower pulled them out. The Holts attacked, and Dan threw a concussive grenade at the two unoccupied goons, but it knocked out the Holts and their thugs. Amy and Dan climbed on the fence, Amy wiring the Franklin Battery to shock the fence and the thugs. They then ran off the isle.
Nellie was furious at the hotel, and Dan spilled about the 39 Clues because he was to tired to lie to Nellie. She decided to help them, Amy looking up the Catacombs, realizing that was the Maze of Bones. They took the Métro to the Denfert-Rochereau station, where they saw Alistair. Nellie hit him, and Alistair explained he tried to save Amy and Dan in Grace's mansion, but Dan was convinced. Alistair offered to have a bite to eat, and over food he asked for Grace's insider tips while he followed them in the Catacombs. Dan said they didn't have any tips, and Alistair saw the Kabras and told them to run under the Barrière d'Enfer and saw bones from 1844, and went deeper until they saw bones from 1785. Dan saw some her numbered, and Amy realized it was a magic box. The Kabras ambushed them and asked for the numbers when Alistair attacked them causing Amy, Dan, and Nellie to escape.
They ran in the twining Catacombs until Nellie's pin flashlight went out. Amy heard a Métro train, and they emerged in a rail for for Métro express trains. Amy and Nellie went on the platform, but Dan's backpack was stuck on the rail, and he was forced to leave it, the picture of his parents lost. They ate, and Amy asked Nellie to ask for the nearest library, and the waiter said to take Métro Line 8 to the École Militaire station. Soon they were looking at Franklin documents in the American Library and Amy found the answer to the magic box at the St. Pierre de Montmarte church. In the rain, they walked up Montmarte to the Sacré-Cœur Basilica, and behind it St. Pierre. Dan found a Lucian crest in the ground, and when they dug the mud up around it, they found a trapdoor to the Catacombs.
Amy and Dan found a mural with Luke, Katherine, Thomas, and Jane, the founders of the branches. Inside a vase was a vial wrapped in sheet music with letters that Dan rearranged to a statement saying that you must energize the vial. Jonah and his dad burst in, and Amy stopped Broderick from filming, and ordered the Wizards to stand by Jane. They ran up to see the Holts drive to the church, then when they opened the door Alistair and Irina ambushed them, but her hit by frozen ice cream thrown by the Holts. Amy and Dan ran up to the belfry and shut the trapdoor, covering it with a bell. Amy went up to energize the vial, and Ian Kabra flew in from the Basilica and tied up Dan. When Amy came down Ian said he was poisoned and gave an 'antidote', for the vial. The trade was made, and Dan was freed he said Ian lied. Eisenhower Holt burst up, but Amy pointed to Ian getting away, but the Holts ran as the police arrived, called by Nellie.
They next day they ate on the Champs-Élysées while William McIntyre came over asking if the Kabras stole the vial, the second lead, ad they admitted yes, acting like they'd not found the clue. William gave Saladin back and left, Amy later revealing to Dan why RESOLUTION was in the clue, because it was an anagram for IRON SOLUTE. Amy brought out the sheet music, and Nellie played it, Dan remembering it as his dad played in his study. It was KV 617, Mozart's last piece of chamber music, and they need to go to Vienna.
On the train Dan looked at the KV 617 music sheet, and found nothing in code, and asked Nellie if they'll stop in every French town, and Nellie added every town in Germany and Austria. The Holts entered the train and Amy and Dan ran, Amy stuffing Saladin and the music sheet in the overhead. The two ran into the mail room and put mail bags against the door, but Eisenhower broke in, briefly stunning Dan while Amy beaned him with a hockey stick. Madison and Regan held the twins up, and upon unwillingness to share the KV 617 sheet's location, Eisenhower began to strangle Dan, but Amy told him where it was. In the overhead, Saladin was found to have shredded the sheet, and the Holts jumped out of the train upon being asked for their tickets. Dan then wrote the music sheet again on a napkin. They pulled in to Vienna, and took a taxi to a hotel where Dan googled the KV 617 sheet, realizing his version had three more stanzas.
The nest day the kids went to Mozarthaus and found no coded messages, but Amy found a Mozart library. Amy searched around and realized Mozart's older sister's diary was in the Mozarthaus. When the librarian went to get Nannerl's diary, it wasn't there and she called in the police. Amy and Dan go Burger King for them and Nellie, and at the hotel saw Jonah Wizard on TV from yesterday bear the Mozarthaus, but his dad wasn't there as we was stealing Nannerl's diary. At the hotel, the three saw Jonah and his dad leave to a DVD party, and Nellie dressed as a chambermaid, Amy and Dan hiding in laundry. At the top floor, the Royal Suite, Nellie was caught as it was the Grand Duke of Luxembourg's room. While she was taken away, Amy and Dan stole away below with Nellie's key card.
In Jonah's suite, they searched for Nannerl's diary frantically, Dan finding a Jonah Kung-Fu Grip figure with a screensaver code, and pocketing it. They search, but find nothing until they see it with the light on in a basket. Dan stands on two phone books, on a chair, on a table, and grabs the diary...but the table and chair break. On the ground, they run seeing Nellie and a guard. They go to the second floor, and jump on an awning, and down, Amy with prodding. In the hotel, Irina comes in saying she'll free Nellie is they hand over what they took from Jonah. Dan hands her the Kung-Fu figure, and she thinks the screensaver code is a vital lead due to her not watching Cartoon Network. Irina then slips out, Nellie coming back five minuets later saying she was let lose. While Nellie was translating Nannerl's diary from German they found that some pages had been cut out. Amy and Dan went to the hotel lobby and played the music hidden on the KV 617 sheet, and an Austrian women sung it, telling them it's called: The Place I was Born. Amy realized it meant where Mozart was born, Salzburg.
The kids get in Nellie's rented Fiat and drive through the Austrian Alps into Salzburg, where Amy stopped Nellie from hitting Alistair running to a tour bus. They drove after him to the Abbey Church of St. Peter, where Amy and Dan got out. They made it to the church's entrance, and the gravesite of Nannerl Mozart. They then saw Alistair's tour group going in the Salzburg Catacombs, so Amy and Dan followed them, and began to press deeper. They passed a tour group with the Man in Black who Amy spotted. As they were in the heart of the tunnels the power turned off, and Amy and Dan held hands as they continued, Dan asking about Hope and Arthur. As Amy talked about Hope there was an explosion. A cave in blocked Amy and Dan from getting back to the church, but they noticed a dull orange glow, and found a trap door into a room. Amy took a piece of old parchment, and they followed the oil lamps to a ladder up which led to a monk dorm.
An elder monk saw the parchment, and they chased Amy and Dan out of the abby, and the jumped in Nellie's Fiat and she drove off. Nellie translated the parchment to the ancient Benedictine wine recipe. Nellie then showed them the homing beacon that was on Saladin, and Amy hatched a plan to get their followers off their trail.