| 0 | - | cover | 1 | pencils: Michael Golden; inks: Michael Golden | Punisher |
| 1 | Special I [Punisher skull] NY Issue! | cover reprint (on interior page) | 1 | pencils: Bill Reinhold; inks: Bill Reinhold | Frank Castle, Punisher |
| 2 | Should a Gentleman Offer a Tiparello to a Lady? | comic story | 22 | script: Mike Baron; pencils: Bill Reinhold; inks: John Nyberg, José Marzán Jr., Tony DeZuniga, M. Ritter; letters: Ken Lopez | Frank Castle, Nick Fury, David Lieberman, Alphonso Mackenzie, Microchip, Punisher |
| 3 | - | cover reprint (on interior page) | 1 | pencils: Ron Wagner; inks: Andy Kubert | Frank Castle, Punisher |
| 4 | St. Paradine's | comic story | 22 | script: Mike Baron; pencils: Mark Texeira; inks: Mark Texeira; letters: Ken Lopez | Frank Castle, David Lieberman, Microchip, Punisher |
| 5 | Germany Has the Autobahn. Now Mexico Has the Slaughter-Bahn! | cover reprint (on interior page) | 1 | pencils: Bill Reinhold; inks: Bill Reinhold | Frank Castle, Punisher |
| 6 | Border Run | comic story | 22 | script: Mike Baron; pencils: Bill Reinhold; inks: Bill Reinhold; letters: Ken Lopez | Frank Castle, Punisher |
| 7 | Star-Spangled Burner! | cover reprint (on interior page) | 1 | pencils: Andy Kubert; inks: Andy Kubert | Frank Castle, Punisher |
| 8 | Flag Burner | comic story | 22 | script: Mike Baron; pencils: Neil Hanson; inks: Neil Hanson; letters: Jade Moede, Ken Lopez | Frank Castle, Punisher |
| 9 | - | cover reprint (on interior page) | 1 | pencils: Ron Wagner; inks: Ron Wagner | Punisher [Frank Castle] |
| 10 | One Way Fare | comic story | 20 | script: Chuck Dixon; pencils: Tod Smith; inks: Danny Bulanadi; letters: Ken Lopez | Punisher [Frank Castle]; Microchip (guest star) |
| 11 | Cold Cache! | cover reprint (on interior page) | 1 | pencils: Hugh Haynes; inks: Bud LaRosa | Punisher [Frank Castle]; Microchip |
| 12 | Cold Cache | comic story | 21 | script: Mike Baron; pencils: Hugh Haynes; inks: Bob Wiacek, Bud La Rosa, Jimmy Palmiotti, Vince Evans, Rodney Ramos, Santiago Oliveras; letters: Ken Lopez | Punisher [Frank Castle]; Microchip (guest star) |
| 13 | Caught--In a Desert Storm! | cover reprint (on interior page) | 1 | pencils: Karl Kesel, Hugh Haynes, John Romita; inks: Terry Austin | Punisher [Frank Castle] |
| 14 | The Brattle Gun Part One | comic story | 20 | script: Mike Baron; pencils: Hugh Haynes; inks: José Marzán Jr.; letters: Ken Lopez | Punisher [Frank Castle]; Microchip (guest star); Saracen (villain); Rose (cameo) |
| 15 | Next Stop: Baghdad! | cover reprint (on interior page) | 1 | pencils: Hugh Haynes; inks: Terry Austin | Punisher [Frank Castle] |
| 16 | The Brattle Gun Part Two | comic story | 20 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Microchip (guest star); Rose (guest star); Saracen (villain) |
| 17 | The Predator Becomes the Prey! | cover reprint (on interior page) | 1 | pencils: Ron Wagner; inks: Andy Kubert | Punisher [Frank Castle] |
| 18 | Death Below Zero | comic story | 22 | script: Chuck Dixon; pencils: Ron Wagner; inks: Ron Wagner; letters: Chris Eliopoulos | Punisher [Frank Castle] |
| 19 | - | cover reprint (on interior page) | 1 | pencils: Michael Golden; inks: Michael Golden | Punisher [Frank Castle] |
| 20 | Yo Yo | comic story | 33 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Microchip (guest star); Yo-Yo Ng (villain) |
| 21 | The Man Takes His War--To Chinatown! | cover reprint (on interior page) | 1 | pencils: Michael Golden; inks: Michael Golden | Punisher [Frank Castle] |
| 22 | Golden Buddah | comic story | 20 | script: Mike Baron; pencils: Tom Morgan; inks: Tom Morgan; colors: Ed Lazellari; letters: Ken Lopez | Punisher [Frank Castle] |
| 23 | Maternity War | cover reprint (on interior page) | 1 | pencils: Mike Harris; inks: Rodney Ramos | Punisher [Frank Castle]; babies |
| 24 | Lupe | comic story | 22 | script: Mike Baron; pencils: Paul Guinan; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Lupe Gutierrez (villain, death) |
| 25 | Final Days Part One: Extortion! | cover reprint (on interior page) | 1 | pencils: Michael Golden; inks: Michael Golden | Punisher [Frank Castle] |
| 26 | The Finger | comic story | 22 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Chris Eliopoulos | Punisher [Frank Castle]; Microchip (guest star); Kingpin [Wilson Fisk] |
| 27 | The Final Days Part Two: Attack! | cover reprint (on interior page) | 1 | pencils: Al Milgrom; inks: Al Milgrom | Punisher [Frank Castle] |
| 28 | The Squeeze | comic story | 20 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Microchip (guest star); Kingpin [Wilson Fisk] (villain); The Mob (villain) |
| 29 | The Final Days Part Three: Conviction! | cover reprint (on interior page) | 1 | pencils: Joe Quesada; inks: Jimmy Palmiotti | Punisher [Frank Castle] (in reflection); Jigsaw [William Russo) |
| 30 | Punisher Plea Bargain | comic story | 21 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Microchip; Jigsaw [William Russo] (villain); Convicts (villains); Gregario (cameo) |
| 31 | The Final Days Part Four: Prison! | cover reprint (on interior page) | 1 | pencils: Joe Quesada; inks: Jimmy Palmiotti | Punisher [Frank Castle] |
| 32 | The Jailhouse Rock | comic story | 22 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Microchip; Jigsaw [William Russo] (villain); Gregario (villain); Convicts (villains); Mike Baron (cameo); Hugh Haynes (cameo); Jimmy Palmiotti (cameo); Marcus David (cameo); Ken Lopez (cameo); Don Daley (cameo); Tom DeFalco (cameo) |
| 33 | The Final Days Part Five: Hunt! | cover reprint (on interior page) | 1 | pencils: Eliot R. Brown; inks: Eliot R. Brown | ? [as Punisher] |
| 34 | America's Most Hunted | comic story | 20 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Microchip (guest star); Gang members (villains) |
| 35 | The Final Days Part Six: Hideout! | cover reprint (on interior page) | 1 | pencils: Michael Golden; inks: Michael Golden | Punisher [Frank Castle]; Doctor Melinda Brewer |
| 36 | The Noose Tightens | comic story | 20 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Microchip; Dr. Melinda Brewer; Kingpin [Wilson Fisk] (villain); The Mob (villain) |
| 37 | The Final Days Part Seven: Requiem... | cover reprint (on interior page) | 1 | pencils: Mark Texeira; inks: Jimmy Palmiotti | Punisher [Frank Castle] |
| 38 | Changes | comic story | 20 | script: Mike Baron; pencils: Hugh Haynes; inks: Jimmy Palmiotti; letters: Ken Lopez | Punisher [Frank Castle]; Microchip; Dr. Melinda Brewer; Kingpin [Wilson Fisk] (villain); The Mob (villain) |
| 39 | The Von Strucker Gambit Part Two | cover reprint (on interior page) | 1 | pencils: Michael Golden; inks: Klaus Janson | Captain America, Frank Castle, Daredevil, Matt Murdock, Punisher, Steve Rogers |
| 40 | The Cutting Edge | comic story | 25 | script: Gregory Wright, Dan Chichester; pencils: John Hebert; inks: Jimmy Palmiotti, Don Hudson, Jim Reddington; letters: Jade Moede | Frank Castle, Nick Fury, Punisher |
| 41 | The System Bytes Part 1 | cover reprint (on interior page) | 1 | pencils: Mark Pacella; inks: Dan Panosian | Punisher |
| 42 | The System Bytes Part 1: Byte by Byte | comic story | 29 | script: Peter David; pencils: Steven Butler; inks: Dan Panosian; letters: Michael Higgins | Punisher; Microchip; Max E. Mumm; Ray Fortuna (villain); Waters (villain); Mazzilli (villain); Smith (villain) |