The Agent Handbook is a book similar to The Black Book of Buried Secrets that contains more information on the world of The 39 Clues. However, it is a bit outdated because it does not have the tenth book information or Amy's and Dan's branch.
The book was released on April 1, 2010. 
The Cahills are the most powerful family in the world, but the source of their power has been lost—scattered around the globe in the form of 39 Clues. The hunt for the Clues has begun and now is YOUR chance to shape history. But, beware—the Clues are in some of the most dangerous locations on earth, hidden by the most famous (and sneakiest) figures of the past 500 years. This Agent Handbook is your secret weapon—it contains all the information your rivals don’t want you to know about the Cahills and the Clues. Just make sure it doesn’t fall into enemy hands...
This handbook has everything you need on the hunt:
- Get never-seen-before Intel about the Cahill branches, including a whole section on the Madrigals!
- Discover insider information about key players.
- Track hidden branch strongholds on your own Agent Map.
- Protect your secrets with 18 pages of codes.
- Forge documents to confuse rival Clue hunters.
Using the given materials, you can "forge" Cahill documents. The Agent Handbook has a section of blank pages that are established as belonging to the certain branch; Ex: Directly following the section of the Lucians, you will find around 20 pages of blank stationary that includes the Lucian Crest, etc. You will notice that in the sections of the book, the stationary resembles that of the notes at the very end of each 39 Clues books, depending on which branch wrote it. An example is one of the Janus stationary; the second stationery is the same stationery used in the last page of 'The Viper's Nest.' So, when the publishers of the Agent Handbook said that you can "Forge documents to confuse rival Clue hunters", they're saying that in the real-life Clue Hunt, you could possibly use the given stationary as "official" paper to use as paper, at the same time confusing rivals of which document is the true, or real, one.
Each branch's sections ultimately have 2 kinds of letterhead stationery; the first is stationary that can be folded along the lines on the back, leading it to look like an ordinary envelope. The second kind is regular paper that simply has the crest of the branch and lines to write on. Sometimes they will have watermarks, as in the Lucian ones.
- On the front cover of the Agent Handbook, there is a brass-like lock holding the chains around the book together. The Madrigal 'M' is engraved into the bottom-right corner of the lock.
- There are many codes in the back of the book that you can crack.
The Agent Handbook comes with one card that is printed into the inside front cover.
|v • d • e The 39 Clues Books|
|The Clue Hunt||The Maze of Bones • One False Note • The Sword Thief • Beyond the Grave • The Black Circle • In Too Deep • The Viper's Nest • The Emperor's Code • Storm Warning • Into the Gauntlet • Vespers Rising|
|Cahills vs. Vespers||The Medusa Plot • A King's Ransom • The Dead Of Night • Shatterproof • Trust No One • Day Of Doom|
|Unstoppable||Nowhere to Run • Breakaway • Countdown • Flashpoint|
|Doublecross||Mission Titanic • Mission Hindenburg • Mission Hurricane • Mission Atomic|
|The Cahill Files||Operation Trinity • The Submarine Job • The Redcoat Chase • The Houdini Escape • Silent Night • Spymasters|
|Rapid Fire||Legacy • Ignition • Hunted • Crushed • Turbulence • Invasion • Fireworks|
|Additional Books||The Black Book of Buried Secrets • Agent Handbook • Midnight Ride • Worlds Collide|
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