| 0 | - | cover | 1 | pencils: Mark Bagley; inks: Vince Russell | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 1 | Collected Editions | promo (ad from the publisher) | 1 | pencils: various; inks: various; colors: various; letters: typeset | |
| 2 | Thunderbolts | filler | 1 | pencils: Mark Bagley; inks: Vince Russell | Masters of Evil |
| 3 | Thunderbolts Classic Credits | credits, title page | 2 | pencils: Mark Bagley; inks: Vince Russell | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 4 | Discover the Shocking Secret Behind Marvel's Newest Champions! | cover reprint (on interior page) | 1 | pencils: Mark Bagley; inks: Vince Russell; letters: Comicraft | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 5 | Justice ... Like Lightning! | comic story | 38 | script: Kurt Busiek; pencils: Mark Bagley; inks: Vince Russell; colors: Joe Rosas; letters: Comicraft, Dave, Oscar Gongora | Atlas, Robbie Baldwin, Black Widow, Bulldozer, Citizen V, Norbert Ebersol, Eliot Franklin, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Namorita, Night Thrasher |
| 6 | Thunderbolts Promotional Image | illustration | 1 | pencils: Mark Bagley; inks: Mark Bagley | Thunderbolts |
| 7 | Introducing the Thunderbolts! | cover reprint (on interior page) | 1 | pencils: Mike Deodato Jr.; inks: Mike Deodato Jr. | Bruce Banner, Hulk, Atlas, Abner Jenkins, Erik Josten, MACH-1 |
| 8 | Introducing the Thunderbolts | comic story | 22 | script: Peter David; pencils: Mike Deodato Jr.; inks: Tom Wegrzyn; colors: Glynis Oliver; letters: Comicraft, KF, RS | Atlas, Bruce Banner, Citizen V, Norbert Ebersol, Melissa Gold, Hulk, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 9 | - | comic story | 1 | script: Peter David; pencils: Jeff Rebner; inks: Tom Wegrzyn; colors: Glynis Oliver; letters: Richard Starkings, Comicraft, KF | Citizen V, Helmut Zemo |
| 10 | The Dawn of a New Age of Heroes! | cover reprint (on interior page) | 2 | pencils: Carlos Pacheco; inks: Scott Koblish | Ka-Zar, Kevin Plunder, Zabu, Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Doctor Strange |
| 11 | - | comic story | 8 | script: Kurt Busiek; pencils: Mark Bagley; inks: Vince Russell; colors: Tom Smith, Graphic Color Works; letters: Janice Chiang | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 12 | - | cover reprint (on interior page) | 1 | pencils: Mark Bagley; inks: Vince Russell; letters: Comicraft | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Mad Thinker, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 13 | Masters of Evil! | cover | 1 | pencils: Mark Bagley; inks: Vince Russell | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 14 | Deceiving Appearances | comic story | 23 | script: Kurt Busiek; pencils: Mark Bagley; inks: Vince Russell; colors: Joe Rosas; letters: Comicraft's Dave Lanphear, OG | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Mad Thinker, Alicia Masters, Meteorite, Franklin Richards, Dallas Riordan, Karla Sofen, Songbird |
| 15 | - | cover reprint (on interior page) | 1 | pencils: Steve Lightle; inks: Steve Lightle; colors: Robb McNabb; letters: Comicraft | Atlas, Citizen V, Norbert Ebersol, Erik Josten, Meteorite, Peter Parker, Karla Sofen, Spider-Man, Techno, Helmut Zemo, Abner Jenkins, MACH-1 |
| 16 | Old Scores | comic story | 38 | script: Kurt Busiek; pencils: Sal Buscema; inks: Dick Giordano; colors: Tom Smith; letters: Comicraft, Dave Lanphear | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, J. Jonah Jameson, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Mary Jane Watson, Peter Parker, Dallas Riordan, Robbie Robertson, Karla Sofen |
| 17 | The New Masters of Evil vs. Thunderbolts | cover reprint (on interior page) | 1 | pencils: Mark Bagley; inks: Vince Russell; letters: Comicraft | Atlas, Citizen V, Norbert Ebersol, Erik Josten, Meteorite, Karla Sofen, Techno, Helmut Zemo, Todd Arliss, Crimson Cowl, Cyclone, Flying Tiger, Pierre Fresson, Melissa Gold |
| 18 | Too Many Masters! | comic story | 22 | script: Kurt Busiek; pencils: Mark Bagley; inks: Vince Russell; colors: Joe Rosas; letters: Comicraft, Dave Lanphear | Atlas, Black Widow, Citizen V, Norbert Ebersol, Erik Josten, Meteorite, Dallas Riordan, Natasha Romanoff, Karla Sofen, Techno, Helmut Zemo, Todd Arliss, Crimson Cowl, Cyclone |
| 19 | Introducing: Jolt | cover reprint (on interior page) | 1 | pencils: Mark Bagley; inks: Vince Russell; letters: Comicraft | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Jolt, Erik Josten, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo, Abner Jenkins, MACH-1, Hallie Takahama |
| 20 | A Shock to the System! | comic story | 22 | script: Kurt Busiek; pencils: Mark Bagley; inks: Vince Russell; colors: Joe Rosas; letters: Dave Lanphear, Comicraft, OG | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Jolt, Erik Josten, MACH-1, Meteorite, Dallas Riordan, Karla Sofen, Songbird, Hallie Takahama, Techno |
| 21 | The Origin of the Thunderbolts | cover | 2 | pencils: Mark Bagley; inks: Vince Russell; letters: Comicraft | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 22 | The Origin of the Thunderbolts! (Chapter 1: Awkward Questions) | comic story | 3 | script: Kurt Busiek; pencils: Mark Bagley; inks: Al Milgrom; colors: Joe Rosas; letters: Dave Lanphear | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Jolt, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Hallie Takahama, Techno, Helmut Zemo |
| 23 | Chapter 2: The Search Begins | comic story | 2 | script: Kurt Busiek; pencils: Bob McLeod; inks: Will Blyberg; colors: Joe Rosas; letters: Dave Lanphear | Baron Zemo, Helmut Zemo |
| 24 | Chapter 3: Technical Support | comic story | 4 | script: Kurt Busiek; pencils: Tom Grummett, Bob McLeod; inks: Scott Koblish, Will Blyberg; colors: Joe Rosas; letters: Dave Lanphear | Baron Zemo, Norbert Ebersol, Fixer, Helmut Zemo |
| 25 | Chapter 4: Screams of Anguish | comic story | 4 | script: Kurt Busiek; pencils: Ron Randall; inks: Jim Sanders III; colors: Joe Rosas; letters: Dave Lanphear | Angar the Screamer, David Angar, Baron Zemo, Melissa Gold, Screaming Mimi, Helmut Zemo |
| 26 | Chapter 5: Shell-Shocked! | comic story | 5 | script: Kurt Busiek; pencils: Gene Colan; inks: Tom Palmer; colors: Joe Rosas; letters: Dave Lanphear | Baron Zemo, Beetle, Daredevil, Abner Jenkins, Matt Murdock, Helmut Zemo |
| 27 | Chapter 6: Onslaught | comic story | 5 | script: Kurt Busiek; pencils: Darick Robertson; inks: Bruce Patterson; colors: Joe Rosas; letters: Dave Lanphear | Bruce Banner, Baron Zemo, Beetle, Captain America, Norbert Ebersol, Falcon, Fixer, Melissa Gold, Ben Grimm, Hulk, Human Torch, Abner Jenkins, Mister Fantastic, Namor |
| 28 | Chapter 7: To Defy a Kosmos | comic story | 4 | script: Kurt Busiek; pencils: George Pérez, Bob McLeod; inks: Karl Kesel, Will Blyberg; colors: Joe Rosas; letters: Dave Lanphear | Baron Zemo, Beetle, Norbert Ebersol, Fixer, Melissa Gold, Goliath, Abner Jenkins, Erik Josten, Kosmos, Screaming Mimi, Helmut Zemo |
| 29 | Chapter 8: Showdown at the Vault | comic story | 11 | script: Kurt Busiek; pencils: Chris Marrinan, Bob McLeod, Mark Bagley; inks: Andrew Pepoy, Will Blyberg, Al Milgrom; colors: Joe Rosas; letters: Dave Lanphear | Armadillo, Atlas, Citizen V, Ann Darnell, Jimmy Darnell, Norbert Ebersol, Melissa Gold, Ironclad, Abner Jenkins, Jolt, Erik Josten, Kaine, Chen Lu, MACH-1 |
| 30 | Thunderbolts Fact File (or, The Truth Behind the Lies) | text article | 1 | script: Kurt Busiek | |
| 31 | Big Trouble! | cover reprint (on interior page) | 1 | pencils: Mark Bagley; inks: Vince Russell; letters: Comicraft | Atlas, Growing Man, Erik Josten, Meteorite, Karla Sofen |
| 32 | Growing Pains | comic story | 22 | script: Kurt Busiek; pencils: Mark Bagley; inks: Vince Russell; colors: Joe Rosas; letters: Comicraft, Dave Lanphear | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Growing Man, Abner Jenkins, Jolt, Erik Josten, MACH-1, Meteorite, Dallas Riordan, Karla Sofen, Songbird, Hallie Takahama |
| 33 | Featuring: Zemo! Namor! | cover reprint (on interior page) | 1 | pencils: Steve Epting; inks: Keith Aiken; letters: Comicraft | Baron Zemo, Citizen V, Namor, Sub-Mariner, Heinrich Zemo, Helmut Zemo |
| 34 | Distant Rumblings! | comic story | 23 | script: Kurt Busiek; pencils: Steve Epting; inks: Bob Wiacek; colors: Tom Smith; letters: Comicraft, Dave Lanphear, OG, SH | Baron Zemo, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, Stan Lee, Namor, Karla Sofen, Sub-Mariner, Hallie Takahama, John Watkins, Heinrich Zemo, Helmut Zemo |
| 35 | - | promo (ad from the publisher) | 1 | | Elizabeth Barstow, Blue Diamond, Citizen V, The Fin, Elton T. Morrow, Peter Noble, Silver Scorpion, John Watkins |
| 36 | Prelude | cover reprint (on interior page) | 1 | pencils: Mark Bagley; inks: Vince Russell | Atlas, Bruce Banner, Hulk, Erik Josten |
| 37 | Thunderbolts: Marvel's Most Wanted TPB | cover reprint (on interior page) | 2 | pencils: Mark Bagley; inks: Scott Hanna; colors: Liquid! | Atlas, Citizen V, Norbert Ebersol, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 38 | Criminal Records | foreword, introduction, preface, afterword | 2 | script: Kurt Busiek | |
| 39 | Citizen V | character profile | 2 | script: Kurt Busiek; pencils: Mark Bagley | Citizen V, Helmut Zemo |
| 40 | Meteorite | character profile | 2 | script: Kurt Busiek; pencils: Mark Bagley | Meteorite, Karla Sofen |
| 41 | M.A.C.H.-1 | character profile | 2 | script: Kurt Busiek; pencils: Mark Bagley | Abner Jenkins, MACH-1 |
| 42 | Songbird | character profile | 2 | script: Kurt Busiek; pencils: Mark Bagley, John Byrne; inks: Joe Sinnott | Melissa Gold, Songbird |
| 43 | Techno | character profile | 2 | script: Kurt Busiek; pencils: Mark Bagley | Norbert Ebersol, Techno |
| 44 | Atlas | character profile | 2 | script: Kurt Busiek; pencils: Mark Bagley | Atlas, Erik Josten |
| 45 | Thunderbolts: Justice Like Lightning TPB | cover reprint (on interior page) | 2 | pencils: Mark Bagley | Atlas, Citizen V, Melissa Gold, Abner Jenkins, Erik Josten, MACH-1, Meteorite, Karla Sofen, Songbird, Techno, Helmut Zemo |
| 46 | The Trickiest Part of the Whole Thing Was Maintaining the Surprise | foreword, introduction, preface, afterword | 1 | script: Kurt Busiek | |
| 47 | Marvel's Most Heroic Collections! | promo (ad from the publisher) | 1 | pencils: various; inks: various; colors: various; letters: typeset | |
| 49 | Justice, Like Lightning! | promo (ad from the publisher) | 1 | pencils: Mark Bagley; inks: Vince Russell | Todd Arliss, Atlas, Citizen V, Crimson Cowl, Cyclone, Norbert Ebersol, Flying Tiger, Pierre Fresson, Melissa Gold, Justine Hammer, Abner Jenkins, Erik Josten, Ulysses Klaue, Klaw |