| 0 | - | cover | 1 | pencils: Dan Duncan; inks: Dan Duncan; colors: Dan Duncan | |
| 1 | - | credits, title page | 3 | letters: typeset | |
| 2 | - | table of contents | 2 | letters: typeset | |
| 3 | Teenage Mutant Ninja Turtles Microseries #6 Cover | cover reprint (on interior page) | 1 | pencils: David Petersen; inks: David Petersen; colors: David Petersen | |
| 4 | - | comic story | 22 | script: Mike Costa, Ben Epstein; pencils: Mike Henderson; inks: Mike Henderson; colors: Ian Herring; letters: Shawn Lee | Casey Jones; Donatello; Hun; Leonardo; Michelangelo; Mrs. Jones; Raphael |
| 5 | Teenage Mutant Ninja Turtles Microseries #6 Mike Henderson Variant Cover | cover reprint (on interior page) | 1 | pencils: Mike Henderson; inks: Mike Henderson; colors: Ian Herring | |
| 6 | Teenage Mutant Ninja Turtles #13 Cover | cover reprint (on interior page) | 1 | pencils: Andy Kuhn; inks: Andy Kuhn; colors: Andy Kuhn | Karai; Foot Clan soldiers |
| 7 | Sins of the Fathers, Part 1 | comic story | 22 | script: Kevin Eastman, Tom Waltz; pencils: Andy Kuhn; inks: Andy Kuhn; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Arnold Jones; Baxter Stockman; Casey Jones; Donatello; Oroku Karai; Leonardo; Michelangelo; Raphael; Shredder; Splinter; Krang |
| 8 | Teenage Mutant Ninja Turtles #13 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Ronda Pattison | |
| 9 | Teenage Mutant Ninja Turtles #14 Cover | cover reprint (on interior page) | 1 | pencils: Andy Kuhn; inks: Andy Kuhn; colors: Andy Kuhn | Splinter |
| 10 | Sins of the Fathers, Part 2 | comic story | 22 | script: Kevin Eastman, Tom Waltz; pencils: Andy Kuhn; inks: Andy Kuhn; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Baxter Stockman; Casey Jones; Krang; Leonardo; Raphael; Shredder; Splinter; Arnold Jones; Donatello; Michelangelo |
| 11 | Teenage Mutant Ninja Turtles #14 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Ronda Pattison | |
| 12 | Teenage Mutant Ninja Turtles Microseries #7 Cover | cover reprint (on interior page) | 1 | pencils: David Petersen; inks: David Petersen; colors: David Petersen | |
| 13 | April | comic story | 22 | script: Barbara Randall Kesel; pencils: Marley Zarcone; inks: Marley Zarcone; colors: Heather Breckel; letters: Shawn Lee | Chet Allen; Donatello; Leonardo; Michelangelo; April O'Neil; Raphael; Mary Wharton |
| 14 | Teenage Mutant Ninja Turtles Microseries #7 Marley Zarcone Variant Cover | cover reprint (on interior page) | 1 | pencils: Marley Zarcone; inks: Marley Zarcone; colors: Marley Zarcone | |
| 15 | Teenage Mutant Ninja Turtles #15 Cover | cover reprint (on interior page) | 1 | pencils: Andy Kuhn; inks: Andy Kuhn; colors: Andy Kuhn | Teenage Mutant Ninja Turtles [Raphael; Leonardo; Michelangelo; Donatello] |
| 16 | Blood Brothers, Part 1 | comic story | 22 | script: Kevin Eastman, Tom Waltz; pencils: Andy Kuhn; inks: Andy Kuhn; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Chet Allan; Lindsey Baker; Donatello; Leonardo; Michelangelo; Raphael; Slash; Casey Jones; Splinter; Woody Dirkins |
| 17 | Teenage Mutant Ninja Turtles #15 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Ronda Pattison | |
| 18 | Teenage Mutant Ninja Turtles #16 Cover | cover reprint (on interior page) | 1 | pencils: Andy Kuhn; inks: Andy Kuhn; colors: Andy Kuhn | Teenage Mutant Ninja Turtles [Raphael; Leonardo; Michelangelo; Donatello]; Mutated snapping turtle |
| 19 | Blood Brothers, Part 2 | comic story | 22 | script: Kevin Eastman, Tom Waltz; pencils: Andy Kuhn; inks: Andy Kuhn; colors: Ronda Pattison; letters: Shawn Lee | Baxter Stockman; Krang; Donatello; Raphael; Michelangelo; Leonardo; Slash; Splinter; Old Hob |
| 20 | Teenage Mutant Ninja Turtles #16 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Ronda Pattison | |
| 21 | Teenage Mutant Ninja Turtles Microseries #8 Cover | cover reprint (on interior page) | 1 | pencils: David Petersen; inks: David Petersen; colors: David Petersen | |
| 22 | - | comic story | 22 | script: Paul Allor; pencils: Paul McCaffrey; inks: Paul McCaffrey; colors: John-Paul Bove; letters: Shawn Lee | Zayton Honeycutt; Shredder; Krang; Baxter Stockman; Granitor; April O'Neil; Casey Jones; Ely Honeycutt; Felix; Leonardo; Marra Honeycutt; Raphael; Splinter |
| 23 | Teenage Mutant Ninja Turtles Microseries #8 Paul McCaffrey Variant Cover | cover reprint (on interior page) | 1 | pencils: Paul McCaffrey; inks: Paul McCaffrey; colors: Paul McCaffrey | |
| 24 | Teenage Mutant Ninja Turtles #17 Cover | cover reprint (on interior page) | 1 | pencils: Ben Bates; inks: Ben Bates; colors: Ben Bates | Teenage Mutant Ninja Turtles [Raphael; Leonardo; Michelangelo; Donatello]; Commander Dansk; Zak; Kala |
| 25 | Krang War, Part 1 | comic story | 22 | script: Kevin Eastman, Tom Waltz; pencils: Ben Bates; inks: Ben Bates; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Casey Jones; Donatello; Karai; Shredder; Honeycutt [Chet Allen]; Krang; Leonardo; Michelangelo; Dask; Queen Gizzla; Kala; Princess Trib; Zak; King Zenter; Raphael; Tragg |
| 26 | Teenage Mutant Ninja Turtles #17 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Ronda Pattison | |
| 27 | Teenage Mutant Ninja Turtles #18 Cover | cover reprint (on interior page) | 1 | pencils: Ben Bates; inks: Ben Bates; colors: Ben Bates | Teenage Mutant Ninja Turtles [Raphael; Leonardo; Michelangelo; Donatello]; Krang |
| 28 | Krang War, Part 2 | comic story | 22 | script: Kevin Eastman, Tom Waltz; pencils: Ben Bates; inks: Ben Bates; colors: Ronda Pattison; letters: Shawn Lee | Donatello; Honeycutt; Krang; Leonardo; Michelangelo; Dask; Gizzla; Kala; Trib; Zak; Zenter; Raphael; April O'Neil; Casey Jones; Splinter; Karai; Baxter Stockman; Lindsey Baker; Emperor Quanin |
| 29 | Teenage Mutant Ninja Turtles #18 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Ronda Pattison | |
| 30 | Teenage Mutant Ninja Turtles #19 Cover | cover reprint (on interior page) | 1 | pencils: Ben Bates; inks: Ben Bates; colors: Ben Bates | Teenage Mutant Ninja Turtles [Raphael; Leonardo; Michelangelo; Donatello]; Commander Dansk; Zak; Kala |
| 31 | Krang War, Part 3 | comic story | 22 | script: Kevin Eastman, Tom Waltz; pencils: Ben Bates; inks: Ben Bates; colors: Ronda Pattison; letters: Shawn Lee | Krang; Honeycutt; Gizzla; Zenter; Trib; Dask; Donatello; Leonardo; Karai; Leonardo; Michelangelo; Raphael; April O'Neil; Casey Jones; Splinter |
| 32 | Teenage Mutant Ninja Turtles #19 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Ronda Pattison | |
| 33 | Teenage Mutant Ninja Turtles #20 Cover | cover reprint (on interior page) | 1 | pencils: Ben Bates; inks: Ben Bates; colors: Ben Bates | |
| 34 | Krang War, Part 4 | comic story | 22 | script: Kevin Eastman, Tom Waltz; pencils: Ben Bates; inks: Ben Bates; colors: Ronda Pattison; letters: Shawn Lee | Raphael; Leonardo; Michelangelo; Donatello; Honeycutt; Zak; Gizzla; Zenter; Kala; Trib; Dask; Krang; Karai |
| 35 | Teenage Mutant Ninja Turtles #20 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Ronda Pattison | |
| 36 | Teenage Mutant Ninja Turtles Villains Micro-Series #1 Cover | cover reprint (on interior page) | 1 | pencils: Tyler Walpole; inks: Tyler Walpole; colors: Tyler Walpole | |
| 37 | - | comic story | 22 | script: Joshua Williamson; pencils: Mike Henderson; inks: Mike Henderson; colors: Ian Herring; letters: Shawn Lee | Krang; Granitor; Tragg; Traxus; Quanin |
| 38 | Teenage Mutant Ninja Turtles Villains Micro-Series #1 Mike Henderson Variant Cover | cover reprint (on interior page) | 1 | pencils: Mike Henderson; inks: Mike Henderson; colors: Ian Herring | |
| 39 | Teenage Mutant Ninja Turtles Villains Micro-Series #2 Cover | cover reprint (on interior page) | 1 | pencils: Tyler Walpole; inks: Tyler Walpole; colors: Tyler Walpole | |
| 40 | - | comic story | 22 | script: Erik Burnham; pencils: Andy Kuhn; inks: Andy Kuhn; colors: John Rauch; letters: Tom B. Long | Baxter Stockman; Flyborg 1.00.1; Krang |
| 41 | Teenage Mutant Ninja Turtles Villains Micro-Series #2 Andy Kuhn Variant Cover | cover reprint (on interior page) | 1 | pencils: Andy Kuhn; inks: Andy Kuhn; colors: Daniel López | |
| 42 | Teenage Mutant Ninja Turtles: The Secret History of the Foot Clan #1 Cover | cover reprint (on interior page) | 1 | pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: Mateus Santolouco | |
| 43 | - | comic story | 22 | script: Mateus Santolouco, Erik Burnham; pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: João "Azeitona" Vieira; letters: Shawn Lee | Alopex; April O'Neil; Casey Jones; Donatello; Karai; Kitsune; Krang; Leonardo; Michelangelo; Patrick Miller; Oroku Maji; Raphael; Shredder; Splinter |
| 44 | Teenage Mutant Ninja Turtles: The Secret History of the Foot Clan #1 Rafael Grampa Variant Cover | cover reprint (on interior page) | 1 | pencils: Rafael Grampá; inks: Rafael Grampá; colors: Rafael Grampá | |
| 45 | Teenage Mutant Ninja Turtles: The Secret History of the Foot Clan #2 Cover | cover reprint (on interior page) | 1 | pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: Mateus Santolouco | |
| 46 | - | comic story | 22 | script: Mateus Santolouco, Erik Burnham; pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: João "Azeitona" Vieira; letters: Shawn Lee | Alopex; April O'Neil; Casey Jones; Donatello; Hamato Yoshi; Karai; Kitsune; Leonardo; Michelangelo; Patrick Miller; Raphael; Shredder; Splinter; Tang Shen |
| 47 | Teenage Mutant Ninja Turtles: The Secret History of the Foot Clan #2 Charles Paul Wilson III Variant Cover | cover reprint (on interior page) | 1 | pencils: CP Wilson III; inks: CP Wilson III; colors: Ryan Browne | |
| 48 | Teenage Mutant Ninja Turtles: The Secret History of the Foot Clan #3 Cover | cover reprint (on interior page) | 1 | pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: Mateus Santolouco | |
| 49 | - | comic story | 22 | script: Mateus Santolouco, Erik Burnham; pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: João "Azeitona" Vieira; letters: Shawn Lee | Alopex; April O'Neil; Casey Jones; Donatello; Karai; Kitsune; Krang; Leonardo; Michelangelo; Patrick Miller; Raphael; Shredder; Splinter |
| 50 | Teenage Mutant Ninja Turtles: The Secret History of the Foot Clan #3 Ross Campbell Variant Cover | cover reprint (on interior page) | 1 | pencils: Ross Campbell; inks: Ross Campbell; colors: Ross Campbell | |
| 51 | Teenage Mutant Ninja Turtles: The Secret History of the Foot Clan #4 Cover | cover reprint (on interior page) | 1 | pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: Mateus Santolouco | |
| 52 | - | comic story | 22 | script: Mateus Santolouco, Erik Burnham; pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: João "Azeitona" Vieira; letters: Shawn Lee | Alopex; April O'Neil; Casey Jones; Donatello; Hamato Yoshi; Karai; Kitsune; Krang; Leonardo; Michelangelo; Patrick Miller; Raphael; Shredder; Splinter |
| 53 | Teenage Mutant Ninja Turtles: The Secret History of the Foot Clan #4 James Harren Variant Cover | cover reprint (on interior page) | 1 | pencils: James Harren; inks: James Harren; colors: James Harren | |
| 54 | Teenage Mutant Ninja Turtles #19 Nick Pitarra Variant Cover | cover reprint (on interior page) | 1 | pencils: Nick Pitarra; inks: Nick Pitarra; colors: Megan Wilson | |
| 55 | Teenage Mutant Ninja Turtles #16 Sophie Campbell Variant Cover | cover reprint (on interior page) | 1 | pencils: Sophie Campbell; inks: Sophie Campbell; colors: Sophie Campbell | |
| 56 | - | illustration | 1 | letters: typeset | |
| 57 | - | illustration | 1 | letters: typeset | |