| 0 | - | cover | 1 | pencils: Dan Duncan; inks: Dan Duncan; colors: Dan Duncan | |
| 1 | - | credits, title page | 4 | letters: typeset | |
| 2 | - | table of contents | 2 | letters: typeset | |
| 3 | Teenage Mutant Ninja Turtles Universe #16 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Jeremy Colwell | |
| 4 | From the Heart, For the Herd, Part 1 | comic story | 20 | script: Chris Mowry; pencils: Giannis Milonogiannis; inks: Giannis Milonogiannis; colors: Lovern Kindzierski; letters: Shawn Lee | Krang; Zog; Zom; Mifor |
| 5 | Teenage Mutant Ninja Turtles Universe #16 Jake Smith Variant Cover | cover reprint (on interior page) | 1 | pencils: Jake Smith; inks: Jake Smith; colors: Jake Smith | |
| 6 | Teenage Mutant Ninja Turtles Universe #17 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Jeremy Colwell | |
| 7 | From the Heart, For the Herd, Part 2 | comic story | 20 | script: Chris Mowry; pencils: Giannis Milonogiannis; inks: Giannis Milonogiannis; colors: Lovern Kindzierski; letters: Shawn Lee | Zog; Zom; Krang |
| 8 | Teenage Mutant Ninja Turtles Universe #17 Giannis Milonogiannis Variant Cover | cover reprint (on interior page) | 1 | pencils: Giannis Milonogiannis; inks: Giannis Milonogiannis; colors: Giannis Milonogiannis | |
| 9 | Teenage Mutant Ninja Turtles Universe #16 Giannis Milonogiannis Variant Cover | cover reprint (on interior page) | 1 | pencils: Giannis Milonogiannis; inks: Giannis Milonogiannis; colors: Giannis Milonogiannis | |
| 10 | Triceratots!, Part 1 | comic story | 4 | script: Erika Anderson; pencils: Michael Dialynas; inks: Michael Dialynas; colors: Michael Dialynas; letters: Chris Mowry | Commander Grel; Zog |
| 11 | Triceratots!, Part 2 | comic story | 4 | script: Erika Anderson; pencils: Michael Dialynas; inks: Michael Dialynas; colors: Michael Dialynas; letters: Chris Mowry | Zaph; Zog; Zola; Zom |
| 12 | Teenage Mutant Ninja Turtles Universe #17 Tony Shasteen Variant Cover | cover reprint (on interior page) | 1 | pencils: Tony Shasteen; inks: Tony Shasteen; colors: Tony Shasteen | |
| 13 | Teenage Mutant Ninja Turtles #76 Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 14 | Invasion of the Triceratons, Part 1 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Damian Couceiro; inks: Damian Couceiro; colors: Ronda Pattison; letters: Shawn Lee | John Bishop; Slash; Commander Zom; Corporal Sherp; Lieutenant Trokk; Sergeant Gord; Donatello; Jennika; Splinter; Kara Lewis; Leonardo; Michelangelo; Raphael; Pepperoni |
| 15 | Teenage Mutant Ninja Turtles #76 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 16 | Teenage Mutant Ninja Turtles #77 Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 17 | Invasion of the Triceratons, Part 2 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Damian Couceiro; inks: Damian Couceiro; colors: Ronda Pattison; letters: Shawn Lee | John Bishop; Donatello; Jennika; Splinter; Leonardo; Michelangelo; April O'Neil; Raphael; Baxter Stockman; Commander Zom; Lieutenant Trokk; Slash |
| 18 | Teenage Mutant Ninja Turtles #77 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 19 | Teenage Mutant Ninja Turtles Universe #18 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Jeremy Colwell | |
| 20 | Monster Hunt | comic story | 20 | script: Paul Allor; pencils: Tyler Boss; inks: Tyler Boss; colors: Ronda Pattison; letters: Shawn Lee | Donatello; Haley; Todd; Leonardo; Michelangelo; Kara Lewis; Raphael |
| 21 | Teenage Mutant Ninja Turtles Universe #18 Tyler Boss Variant Cover | cover reprint (on interior page) | 1 | pencils: Tyler Boss; inks: Tyler Boss; colors: Tyler Boss | |
| 22 | Teenage Mutant Ninja Turtles #77 Valentine De Landro Variant Cover | cover reprint (on interior page) | 1 | pencils: Valentine DeLandro; inks: Valentine DeLandro; colors: Valentine DeLandro | |
| 23 | Mutagen Maintenance | comic story | 4 | script: Caleb Goellner; pencils: Michael Dialynas; inks: Michael Dialynas; colors: Michael Dialynas; letters: Shawn Lee | Lindsey Baker; Herman the Hermit Crab; Old Hob; Mondo Gecko; Pete; Seymour Gutz |
| 24 | Teenage Mutant Ninja Turtles Universe #18 Ron Chan Variant Cover | cover reprint (on interior page) | 1 | pencils: Ron Chan; inks: Ron Chan; colors: Ron Chan | |
| 25 | Teenage Mutant Ninja Turtles #78 Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 26 | Invasion of the Triceratons, Part 3 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Damian Couceiro; inks: Damian Couceiro; colors: Ronda Pattison; letters: Shawn Lee | Donatello; Jennika; Splinter; Hun; Leonardo; Michelangelo; Kara Lewis; Casey Jones; Link; Malo; Raphael; Corporal Raon; Udok; Commander Zom; Agent John Bishop; Senator Robert Lawson; Lester; Beth O'Neil; John O'Neil; Burne Thompson |
| 27 | Teenage Mutant Ninja Turtles #78 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 28 | Teenage Mutant Ninja Turtles Universe #21 Nathan Greno Variant Cover | cover reprint (on interior page) | 1 | pencils: Nathan Greno; inks: Nathan Greno; colors: Sabine Rich | |
| 29 | How Woody Spent His Triceraton Invasion | comic story | 4 | script: Caleb Goellner; pencils: Pablo Tunica; inks: Pablo Tunica; colors: Patricio Delpeche; letters: Shawn Lee | Woody Dirkins; John O'Neil; Rupert |
| 30 | Teenage Mutant Ninja Turtles #78 Kelly Williams Variant Cover | cover reprint (on interior page) | 1 | pencils: Kelly Williams; inks: Kelly Williams; colors: Kelly Williams | |
| 31 | Teenage Mutant Ninja Turtles #79 Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 32 | Invasion of the Triceratons, Part 4 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Brahm Revel; inks: Brahm Revel; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Baxter Stockman; Donatello; John Bishop; Slash; Beth O'Neil; Jennika; Splinter; John O'Neil; Leonardo; Michelangelo; Raphael; Commander Zom |
| 33 | Teenage Mutant Ninja Turtles #79 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 34 | Teenage Mutant Ninja Turtles #80 Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 35 | Invasion of the Triceratons, Part 5 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Brahm Revel; inks: Brahm Revel; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Baxter Stockman; Donatello; Agent John Bishop; Slash; Leonardo; Michelangelo; Man Ray; Old Hob; Hun; Casey Jones; Raphael; Zom; Burne Thompson; Beth O'Neil; John O'Neil; Kara Lewis |
| 36 | Teenage Mutant Ninja Turtles #80 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 37 | Teenage Mutant Ninja Turtles Universe #21 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Jeremy Colwell | |
| 38 | Lost Causes, Part 1 | comic story | 20 | script: Paul Allor; pencils: Mark Torres; inks: Mark Torres; colors: Ronda Pattison; letters: Shawn Lee | Churk; Donatello; Drel; Kleve; Ma'riell; Yot; Zom; Ch'rell |
| 39 | Teenage Mutant Ninja Turtles Universe #21 Mark Torres Variant Cover | cover reprint (on interior page) | 1 | pencils: Mark Torres; inks: Mark Torres; colors: Mark Torres | |
| 40 | Teenage Mutant Ninja Turtles Universe #22 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Jeremy Colwell | |
| 41 | Lost Causes, Part 2 | comic story | 20 | script: Paul Allor; pencils: Mark Torres; inks: Mark Torres; colors: Ronda Pattison; letters: Shawn Lee | Donatello; Drel; Kleve; Leatherhead; Ma'riell; Tarsa; Zom; Ch'rell |
| 42 | Teenage Mutant Ninja Turtles Universe #22 Mark Torres Variant Cover | cover reprint (on interior page) | 1 | pencils: Mark Torres; inks: Mark Torres; colors: Mark Torres | |
| 43 | Teenage Mutant Ninja Turtles Universe #22 Fico Ossio Variant Cover | cover reprint (on interior page) | 1 | pencils: Fico Ossio; inks: Fico Ossio; colors: Fico Ossio | |
| 44 | Dangerous Waters | comic story | 4 | script: Ross May; pencils: Chris Johnson; inks: Chris Johnson; colors: Mark Englert; letters: Shawn Lee | Leatherhead |
| 45 | Teenage Mutant Ninja Turtles Universe #22 Tim Lattie Variant Cover | cover reprint (on interior page) | 1 | pencils: Tim Lattie; inks: Tim Lattie; colors: Tim Lattie | |
| 46 | Teenage Mutant Ninja Turtles Universe #23 Marco Itri Variant Cover | cover reprint (on interior page) | 1 | pencils: Marco Itri; inks: Marco Itri; colors: Brittany Peer | |
| 47 | Nobody Cares | comic story | 4 | script: Rich Douek; pencils: Brahm Revel; inks: Brahm Revel; colors: Brahm Revel; letters: Shawn Lee | Angel Bridge; Zodi |
| 48 | Teenage Mutant Ninja Turtles Macroseries #1 Ryan Brown Variant Cover | cover reprint (on interior page) | 1 | pencils: Ryan Brown; inks: Ryan Brown; colors: Ryan Brown | Donatello |
| 49 | Teenage Mutant Ninja Turtles #81 Cover | cover reprint (on interior page) | 1 | pencils: Dave Wachter; inks: Dave Wachter; colors: Dave Wachter | Rat King |
| 50 | Kingdom of Rats Prelude | comic story | 4 | script: Bobby Curnow; pencils: Pablo Tunica; inks: Pablo Tunica; colors: Pablo Tunica; letters: Shawn Lee | Rat King |
| 51 | Kingdom of Rats, Part 1 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Dave Wachter; inks: Dave Wachter; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Baxter Stockman; Donatello; Jennika; Splinter; Bullet; Fade; Hun; John Bishop; Michelangelo; Casey Jones; Raphael; Rat King; Brooklyn S. Bridge; Burne Thompson; Alberto; Kara Lewis; Slash; Toad Baron |
| 52 | Teenage Mutant Ninja Turtles #81 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 53 | Teenage Mutant Ninja Turtles #82 Cover | cover reprint (on interior page) | 1 | pencils: Dave Wachter; inks: Dave Wachter; colors: Dave Wachter | Rat King |
| 54 | Kingdom of Rats, Part 2 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Dave Wachter; inks: Dave Wachter; colors: Ronda Pattison; letters: Shawn Lee | Baxter Stockman; Donatello; Alberto; Bob; Franz; John Bishop; Leonardo; Michelangelo; Raphael; Rat King; Toad Baron; Jennika; Kara Lewis; Manmoth; Slash; Splinter |
| 55 | Teenage Mutant Ninja Turtles #82 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 56 | Teenage Mutant Ninja Turtles #83 Cover | cover reprint (on interior page) | 1 | pencils: Dave Wachter; inks: Dave Wachter; colors: Dave Wachter | Rat King |
| 57 | Kingdom of Rats, Part 3 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Dave Wachter; inks: Dave Wachter; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Baxter Stockman; Casey Jones; Donatello; Hun; Jennika; Leonardo; Lupo; Manmoth; Michelangelo; Raphael; Rat King; Irma Langenstein |
| 58 | Teenage Mutant Ninja Turtles #83 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 59 | Teenage Mutant Ninja Turtles #84 Cover | cover reprint (on interior page) | 1 | pencils: Dave Wachter; inks: Dave Wachter; colors: Dave Wachter | Rat King |
| 60 | Kingdom of Rats, Part 4 | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Dave Wachter; inks: Dave Wachter; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Baxter Stockman; Donatello; Leonardo; Michelangelo; Rat King; Raphael; Jennika; Splinter |
| 61 | Teenage Mutant Ninja Turtles #84 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Tomi Varga | |
| 62 | Teenage Mutant Ninja Turtles Macroseries #1 Cover | cover reprint (on interior page) | 1 | pencils: David Petersen; inks: David Petersen; colors: David Petersen | Donatello |
| 63 | - | comic story | 40 | script: Paul Allor; pencils: Brahm Revel; inks: Brahm Revel; colors: Cris Peter; letters: Shawn Lee | Donatello; Harold Lilja; Metalhead; Baxter Stockman; Bebop; Libby Meitner; Manmoth; Null; Rocksteady |
| 64 | - | illustration | 1 | | |
| 65 | - | illustration | 1 | letters: typeset | |