| 0 | - | cover | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo | Enigma |
| 1 | Endpapers | illustration | 2 | pencils: Duncan Fegredo; inks: Duncan Fegredo | |
| 2 | - | blank page(s) | 1 | | |
| 3 | Title Page | credits, title page | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo | Enigma |
| 4 | - | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo | Enigma |
| 5 | Credits | credits, title page | 1 | letters: typeset | |
| 6 | A Straight Man Walks into a Gay Bar... | foreword, introduction, preface, afterword | 2 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo | |
| 7 | Chapter 1: The Lizard, The Head, The Enigma | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 8 | Enigma #1 Cover | cover reprint (on interior page) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 9 | Chapter 1: The Lizard, The Head, The Enigma | comic story | 24 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Sherilyn Van Valkenburgh; letters: John Costanza | Michael Smith (first appearance); Enigma (first appearance); Sandra (first appearance); Victor Lamont (first appearance); Frank (first appearance); Bob (first appearance, death); Joe (first appearance); The Head [Roger Cliff] (first appearance, villain) |
| 10 | Chapter 2: The Truth | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma; The Truth [Victor Lamont] |
| 11 | Enigma #2 Cover | cover reprint (on interior page) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 12 | Chapter 2: The Truth | comic story | 24 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Sherilyn Van Valkenburgh; letters: John Costanza | Enigma; Michael Smith; Sandra; Craig (first appearance); Mulligan (first appearance); The Truth [Victor Lamont] (villain); The Head [Roger Cliff] (villain, death) |
| 13 | Chapter 3: The Good Boy | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma; Envelope Girl [Victoria Yes] |
| 14 | Enigma #3 Cover | cover reprint (on interior page) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 15 | Chapter 3: The Good Boy | comic story | 24 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Sherilyn Van Valkenburgh; letters: John Costanza | Enigma; Michael Smith; Titus Bird (first appearance); Sandra; Mrs. Smith (flashback); Joe; Saturn (first appearance); William Williams (first appearance); Envelope Girl [Victoria Yes] (first appearance, villain); The Truth [Victor Lamont] (villain) |
| 16 | Chapter 4: ...And Then What? | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 17 | Enigma #4 Cover | cover reprint (on interior page) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 18 | Chapter 4: ...And Then What? | comic story | 24 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Sherilyn Van Valkenburgh; letters: John Costanza | Enigma; Michael Smith; Titus Bird; Sandra; John Cade (first appearance, death); The Enigmatics; Envelope Girl [Victoria Yes] (villain); The Truth [Victor Lamont] (villain) |
| 19 | Chapter 5: Lizards and Ghosts | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma; The Interior League |
| 20 | Enigma #5 Cover | cover reprint (on interior page) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 21 | Chapter 5: Lizards and Ghosts | comic story | 24 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Sherilyn Van Valkenburgh; letters: John Costanza | Enigma; Michael Smith; Titus Bird; The Enigmatics; The Interior League (first appearance, villains); Envelope Girl [Victoria Yes] (villain) |
| 22 | Chapter 6: The End of the World | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 23 | Enigma #6 Cover | cover reprint (on interior page) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 24 | Chapter 6: The End of the World | comic story | 24 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Sherilyn Van Valkenburgh; letters: John Costanza | Enigma; Michael Smith; Titus Bird; Stephen (first appearance, flashback); Envelope Girl [Victoria Yes] (villain) |
| 25 | Chapter 7: Sex in Arizona | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma; Michael Smith |
| 26 | Enigma #7 Cover | cover reprint (on interior page) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 27 | Chapter 7: Sex in Arizona | comic story | 24 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Sherilyn Van Valkenburgh; letters: John Costanza | Enigma; Michael Smith; Titus Bird; Mrs. Smith (flashback); Victoria Yes [also as Enigma's mother] (villain) |
| 28 | Chapter 8: Queer | illustration | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma; Michael Smith |
| 29 | Enigma #8 Cover | cover reprint (on interior page) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 30 | Chapter 8: Queer | comic story | 24 | script: Peter Milligan; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Sherilyn Van Valkenburgh; letters: John Costanza | Enigma (origin); Michael Smith; Titus Bird; Doug Moon (first appearance, flashback); Enigma's mother |
| 31 | Secret Origins or a Brief History of Style | foreword, introduction, preface, afterword | 2 | script: Duncan Fegredo; pencils: Duncan Fegredo; inks: Duncan Fegredo | |
| 32 | Sketchbook | illustration | 8 | script: Art Young, Duncan Fegredo; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo; letters: Todd Klein, Richard Bruning | Enigma |
| 33 | Reading a Comic | text article | 24 | script: Duncan Fegredo; pencils: Duncan Fegredo, Sherilyn Van Valkenburgh; inks: Duncan Fegredo, Sherilyn Van Valkenburgh; colors: Sherilyn Van Valkenburgh | |
| 34 | Cover Creation | text article | 2 | script: Duncan Fegredo; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | |
| 35 | Original Comic Covers | cover reprint (on interior page) | 2 | pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | enigma |
| 36 | The Vertigo Gallery Book | text article | 2 | script: Duncan Fegredo; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo, Daniel Vozzo | Enigma |
| 37 | Trading Card | text article | 1 | script: Duncan Fegredo; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 38 | 1st Collected Edition | text article | 4 | script: Duncan Fegredo; pencils: Duncan Fegredo; inks: Duncan Fegredo; colors: Duncan Fegredo | Enigma |
| 39 | New Cover | text article | 1 | script: Duncan Fegredo; pencils: Duncan Fegredo; inks: Duncan Fegredo | |
| 40 | Promotional Art | text article | 1 | script: Duncan Fegredo; pencils: Duncan Fegredo; inks: Duncan Fegredo | Enigma |
| 41 | Creator Bios | text article | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo | |
| 42 | Berger Books | promo (ad from the publisher) | 2 | script: ? (promo copy); pencils: various; inks: various; colors: various; letters: typeset | |
| 43 | Copyright Page | statement of ownership | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo | |
| 44 | - | blank page(s) | 1 | | |
| 45 | Endpapers | illustration | 2 | pencils: Duncan Fegredo; inks: Duncan Fegredo | |
| 48 | Back Cover | promo (ad from the publisher) | 1 | pencils: Duncan Fegredo; inks: Duncan Fegredo | |