| 0 | Plague of Frogs 2 | cover | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | |
| 1 | B.P.R.D. | promo (ad from the publisher) | 1 | letters: typeset | |
| 2 | Bureau for Paranormal Research and Defense | character profile | 1 | pencils: Guy Davis; inks: Guy Davis | Benjamin Daimio; Roger the Homunculus; Abe Sapien; Liz Sherman; Kate Corrigan; Johann Kraus |
| 3 | Plague of Frogs Volume Two | credits, title page | 2 | letters: typeset | |
| 4 | Introduction | foreword, introduction, preface, afterword | 1 | script: Scott Allie | |
| 5 | Book One The Dead | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | |
| 6 | The Dead | credits, title page | 1 | letters: typeset | |
| 7 | Prologue | illustration | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Johann Kraus; Liz Sherman; Abe Sapien; Roger the Homunculus; Kate Corrigan |
| 8 | Born Again | comic story | 8 | script: Mike Mignola, John Arcudi; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Liz Sherman; Roger the Homunculus; Abe Sapien; Johann Kraus |
| 9 | Chapter One | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Abe Sapien |
| 10 | The Dead [Part 1] | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger; Johann Kraus; Ben Daimio |
| 11 | Chapter Two | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Abe Sapien; Liz Sherman; Ben Daimio |
| 12 | - | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger; Johann Kraus; Ben Daimio |
| 13 | Chapter Three | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Johann Kraus |
| 14 | - | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger; Johann Kraus; Ben Daimio |
| 15 | Chapter Four | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Liz Sherman; Roger; Johann Kraus |
| 16 | - | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger; Johann Kraus; Ben Daimio |
| 17 | Chapter Five | cover reprint (on interior page) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | Abe Sapien |
| 18 | - | comic story | 24 | script: Mike Mignola; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Abe Sapien; Dr. Kate Corrigan; Liz Sherman; Roger; Johann Kraus; Ben Daimio |
| 19 | Book Two War on Frogs | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | |
| 20 | Chapter One | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | |
| 21 | - | credits, title page | 1 | letters: typeset | |
| 22 | The Black Flame | comic story | 24 | script: Mike Mignola, John Arcudi; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Captain Benjamin Daimio; Roger; Liz Sherman; Abe Sapien; Johann Kraus; Dr. Kate Corrigan |
| 23 | Chapter Two | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart; letters: Amy Arendts | Roger the Homunculus |
| 24 | - | credits, title page | 1 | letters: typeset | |
| 25 | War on Frogs [Part 1] | comic story | 24 | script: John Arcudi; pencils: Herb Trimpe; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | |
| 26 | Chapter Three | illustration | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | |
| 27 | - | credits, title page | 1 | letters: typeset | |
| 28 | - | comic story | 24 | script: Mike Mignola, John Arcudi; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Ben Daimio |
| 29 | Chapter Four | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart; letters: Amy Arendts | |
| 30 | - | credits, title page | 1 | letters: typeset | |
| 31 | War on Frogs [Chapter 2] | comic story | 24 | script: John Arcudi; pencils: John Severin; inks: John Severin; colors: Dave Stewart; letters: Clem Robins | |
| 32 | Chapter Five | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart; letters: Amy Arendts | Johann Kraus |
| 33 | - | credits, title page | 1 | letters: typeset | |
| 34 | War on Frogs [Chapter 4] | comic story | 24 | script: John Arcudi; pencils: Peter Snejbjerg; inks: Peter Snejbjerg; colors: Bjarne Hansen; letters: Clem Robins | |
| 35 | Book Three The Black Flame | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | |
| 36 | The Black Flame | credits, title page | 1 | letters: typeset | |
| 37 | Chapter One | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Roger |
| 38 | The Black Flame | comic story | 24 | script: Mike Mignola, John Arcudi; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Captain Benjamin Daimio; Roger; Liz Sherman; Abe Sapien; Johann Kraus; Dr. Kate Corrigan; Landis Pope [The Black Flame] (introduction) |
| 39 | Chapter Two | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Roger the Homunculus; The Black Flame [Landis Pope] |
| 40 | The Black Flame | comic story | 24 | script: Mike Mignola, John Arcudi; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Captain Benjamin Daimio; Roger the Homunculus (death); Liz Sherman; Abe Sapien; Johann Kraus; Dr. Kate Corrigan; Landis Pope [The Black Flame] |
| 41 | Chapter Three | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Abe Sapien |
| 42 | The Black Flame | comic story | 24 | script: Mike Mignola, John Arcudi; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Captain Benjamin Daimio; Roger the Homunculus (body only); Liz Sherman; Abe Sapien; Johann Kraus; Dr. Kate Corrigan; The Black Flame [Landis Pope] |
| 43 | Chapter Four | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | Liz Sherman; Johann Kraus |
| 44 | - | comic story | 24 | script: Mike Mignola, John Arcudi; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Captain Benjamin Daimo; Liz Sherman; Abe Sapien; Johann Kraus; Dr. Kate Corrigan; The Black Flame [Landis Pope] |
| 45 | Chapter Five | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | The Black Flame [Landis Pope] |
| 46 | The Black Flame | comic story | 24 | script: Mike Mignola, John Arcudi; pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart; letters: Clem Robins | Captain Benjamin Daimo; Roger the Homunculus (body only); Liz Sherman; Abe Sapien; Johann Kraus; Dr. Kate Corrigan; The Black Flame [Landis Pope] |
| 47 | Epilogue | cover reprint (on interior page) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart; letters: Amy Arendts | Liz Sherman |
| 48 | - | credits, title page | 1 | letters: typeset | |
| 49 | War on Frogs [Chapter 3] | comic story | 24 | script: John Arcudi; pencils: Karl Moline; inks: Karl Moline; colors: Dave Stewart; letters: Clem Robins | |
| 50 | Afterword | foreword, introduction, preface, afterword | 1 | script: Mike Mignola | |
| 51 | The Dead Sketchbook | illustration | 20 | script: Guy Davis; pencils: Guy Davis; letters: Guy Davis | |
| 52 | The Black Flame Sketchbook | illustration | 11 | script: Guy Davis; pencils: Guy Davis; letters: Guy Davis | |
| 53 | War on Frogs Sketchbook | illustration | 8 | script: Scott Allie; pencils: Herb Trimpe, Guy Davis, Karl Moline; inks: Herb Trimpe, Guy Davis, Karl Moline; colors: Dave Stewart; letters: Guy Davis | |
| 54 | Recommended Dark Horse Reading | promo (ad from the publisher) | 1 | pencils: various; inks: various; colors: various; letters: typeset | |
| 55 | Hellboy by Mike Mignola | promo (ad from the publisher) | 1 | pencils: Mike Mignola; inks: Mike Mignola; colors: Dave Stewart | |
| 56 | Mike Mignola | text article | 1 | letters: typeset | |
| 57 | back cover | promo (ad from the publisher) | 1 | pencils: Guy Davis; inks: Guy Davis; colors: Dave Stewart | |