Missions are short games on the 39 Clues website. Some missions have completely new characters, while some have characters from the books. Each mission has a card combination that does not unlock the Clue if you have not finished the mission. All Missions unlock a clue except 10 which gives you Madrigal status and all of the Cahills vs. Vespers Missions.
This mission is located outside of Grace's (burned down) house. William McIntyre will introduce you to the Cahill branches and you must play a mini game about every branch (including Madrigal, but of course, it is disguised as merely Cahill) and after you succeed you will get a secret code and you must input that code. The clue discovered in this mission is Uranium.
Mission 1 is located in Drumnadrocit in the United Kingdom. It is set to the 1st format, where the "talking" is just spamming the word TALK on the bottom of the page. In this mission you will be finding a Clue lost on the Titanic, where Anne Cahill was believed to have died. The card related to this are The Titanic, Paul McPherson and 4 others. The Ekaterina clue discovered is Phosphorus.
In this Mission you will be going to the Ekaterina stronghold in Cairo, Egypt. You are tricked by Ian Kabra and then later saved.Then you must rebuild a mechanical dog. The Ekaterina Clue discovered is Silver.
Mission 9 is named "Cliffhanger Clue" and you willl be tracking the famous singer Josephine Baker. Reagan Holt will help you but Madison will be demanding to know where the Clue is. This mission references Taylor Lautner. The Lucian clue discovered is Mint.
Mission 10 is called "End Game" and you will have to have all 39 Clues before you can complete the mission.
At the start of this mission, you will be at Tikal, Guatemala where you must turn stones to form the letter M for Madrigal, at which point a door will open and you will have to answer 10 questions based on the books in order to progress. After you have answered the 10th question, Dan will send you a message on your PDA (Personal Digital Assistant) giving you a chance to become a Madrigal, just like him. Then you will see a 39 Clues passport with four plane tickets.
The red one will take you to United Nations Headquarters where Natalie will give you a test to test your puzzle solving skills. You must earn 6000 points to pass. To earn points, you must successfully unscramble phrases in a limited timeframe.
The yellow one will take you to where Grace's mansion once stood where Alistair will give you a test to test your hacking skills. You must earn 250 points to pass. This is similar to the game where you must use a platform to keep the ball bouncing and hit bricks.
The blue one will take you to Madagascar where Hamilton will give you a test to test your precision skills. You must earn 150 points to pass. To earn points you must shoot hoops from different angles in a limited timeframe.
The green one will take you to Easter Island where Jonah will give you a test to test your visual puzzle solving skills. You must earn 8000 points to pass. For this challenge, you must match up blocks on a cube.
After those you will get another message from Dan, telling you that you are officially a Madrigal now.
Mission 11 is called, "Behind Enemy Lines" and can only be unlocked by digitizing all of the cards that come with Book 11, "Vespers Rising". In it, you have to track down Vesper agent Casper Wyoming and see if he has left any important documents after attempting to capture Amy and Dan. At the end of the mission, you retrieve secret information about the Vesper inner circle, which is called "The Council of Six"and the Cipher for Vesper Transmission. There is also a short story showing Damien Vesper's pursuit of great things, and about how servants he thought were lying were beheaded, and about how servants he thought were telling the truth were rewarded generously (the Vespers wrote this, so he probably just gave the family enough for a poor meal, but that's really nice for Damien Vesper.)
The Acropolis Raid is a mission that introduces you to Cahills vs. Vespers.
If you complete it, you are granted the status of a member of the Saladin League, an elite team of Cahills that help stop the Vespers.
In this Mission you have to identify the Vesper Enforcer from the characters in Card 266: Vesper Enforcer. You allowed to have one freebie and in the end you find out that the Enforcer is Cassandra Prince, an alias for Cheyenne Wyoming, Casper Wyoming's twin sister.
This mission you will discover the identity of Vesper 5, the Spymaster. The suspects are from Card 272: The Vesper Spymaster. In the end you will find out Vesper 5 is Luna Amato, the partner of Milos Vanek. She also works at Interpol.
This mission is going to be released with Cahills vs. Vespers book 3:The Dead Of Night and in it you will have to unmask Vesper 4 - The Scientist. Suspects: Sandy Bancroft, Mark Rosenbloom, Bartu Yilmaz, Ned Starling, Salim Umarov, unknown suspect (later turns out to be Ian Kabra). Vesper 4 is Sandy Bancroft.
This mission is going to be released with Cahills vs. Vespers book 4 and in it you will have to unmask Vesper 3 - The Mole Suspects: Evan Tolliver, Sinead Starling, Ian Kabra, Hamilton Holt, Jake Rosenbloom, and Jonah Wizard. Vesper 3 is Sinead Starling.
This mission is going to be released with Cahills vs. Vespers book 5: Trust No One, and in it you will have to unmask Vesper 2 - The Shield. Suspects: LaCher Siffright, Isabel Kabra, Jake Rosenbloom, Dave Speminer, Beatrice Cahill and Arthur Trent. Vesper 2 is revealed to be Isabel Kabra.
This mission was released with Day of Doom, and in it you have to destroy any remaining Vesper strongholds so they will never rise again.
In this mission, you have to track down a armilary sphere and give it to the Vespers.
This mission is unlocked by adding the cards from Cahills vs. Vespers Card Pack 1: The Marco Polo Heist, released with Cahills vs. Vespers Book 1: The Medusa Plot.
In this mission, you have to track down an ancient gear and give it to the Vespers.
This mission is unlocked by adding the cards from Cahills vs. Vespers Card Pack 2: The Magellan Heist, released with Cahills vs. Vespers Book 4: Shatterproof.