Ex Machina is the story of Mitchell Hundred, the world's first and only superhero, who, after his intervention during the 9/11 attacks, is elected Mayor of New York City. Before becoming Mayor he was known as The Great Machine, a hero who can communicate with and command any machine. The story takes place during his term in office but is also cut with flashbacks that are integral to the story being told. The book is known for exploring varying political and religious issues as well as unfolding the mysteries regarding Mitch's powers.

The series won the 2005 Eisner Award for Best New Series. Brian K. Vaughan won the Best Writer Award that year in part for his work on Ex Machina.

Trade Paperbacks

• The First Hundred Days (#1-5)
• Ex Machina Compendium Book One (#1-25)
• Tag (#6-10)
• Fact v. Fiction (#11-16)
• March to War (#17-20 and Ex Machina Special #1-2)
• Smoke Smoke ( #21-25)
• Power Down (#26-29 and Inside the Machine)
• Ex Machina Compendium Book Two (#26-50)
• Ex Cathedra (#30-34)
• Dirty Tricks (#35-39 and Ex Machina Special #3)
• Ring out the Old (#40-44 and Ex Machina Special #4)
• Term Limits (#45-50)

Deluxe Hardcovers

• Ex Machina Deluxe Edition Book One (#1-11)
• Ex Machina: The Complete Series Omnibus (#1-50)
• Ex Machina Deluxe Edition Book Two (#12-20 and Ex Machina Special #1-2)
• Ex Machina Deluxe Edition Book Three (#21-29, Ex Machina: Inside the Machine, and Ex Machina Special #3)
• Ex Machina Deluxe Edition Book Four (#30-40)
• Ex Machina Deluxe Edition Book Five (#41-50 and Ex Machina Special #4)