| 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 | Bebop & Rocksteady Destroy Everything #1 Cover | cover reprint (on interior page) | 1 | pencils: Nick Pitarra; inks: Nick Pitarra; colors: Michael Garland | |
| 4 | Bebop and Rocksteady Destroy Everything | comic story | 20 | script: Ben Bates, Dustin Weaver; pencils: Sophie Campbell, Dustin Weaver, Ben Bates, Giannis Milonogiannis; inks: Sophie Campbell, Dustin Weaver, Ben Bates, Giannis Milonogiannis; colors: Bill Crabtree, Sophie Campbell; letters: Shawn Lee | |
| 5 | Bebop & Rocksteady Destroy Everything #1 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Dustin Weaver; inks: Dustin Weaver; colors: Dustin Weaver | |
| 6 | Bebop & Rocksteady Destroy Everything #2 Cover | cover reprint (on interior page) | 1 | pencils: Nick Pitarra; inks: Nick Pitarra; colors: Michael Garland | |
| 7 | - | comic story | 20 | script: Ben Bates, Dustin Weaver; pencils: Ben Bates, Giannis Milonogiannis, Sophie Campbell; inks: Ben Bates, Giannis Milonogiannis, Sophie Campbell; colors: Bill Crabtree, Sophie Campbell; letters: Shawn Lee | |
| 8 | Bebop & Rocksteady Destroy Everything #2 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Sophie Campbell; inks: Sophie Campbell; colors: Sophie Campbell | |
| 9 | Bebop & Rocksteady Destroy Everything #3 Cover | cover reprint (on interior page) | 1 | pencils: Nick Pitarra; inks: Nick Pitarra; colors: Michael Garland | |
| 10 | - | comic story | 20 | script: Ben Bates, Dustin Weaver; pencils: Ben Bates, Damian Couceiro; inks: Ben Bates, Damian Couceiro; colors: Bill Crabtree; letters: Shawn Lee | |
| 11 | Bebop & Rocksteady Destroy Everything #3 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 12 | Bebop & Rocksteady Destroy Everything #4 Cover | cover reprint (on interior page) | 1 | pencils: Nick Pitarra; inks: Nick Pitarra; colors: Michael Garland | |
| 13 | - | comic story | 20 | script: Ben Bates, Dustin Weaver; pencils: Dustin Weaver, Nick Pitarra, Ben Tiesma, Damian Couceiro, Pablo Tunica, Tadd Galusha; inks: Dustin Weaver, Nick Pitarra, Ben Tiesma, Damian Couceiro, Pablo Tunica, Tadd Galusha; colors: Bill Crabtree, Michael Garland, Jean-François Beaulieu; letters: Shawn Lee | |
| 14 | Bebop & Rocksteady Destroy Everything #4 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Ben Bates; inks: Ben Bates; colors: Ben Bates | |
| 15 | Bebop & Rocksteady Destroy Everything #5 Cover | cover reprint (on interior page) | 1 | pencils: Nick Pitarra; inks: Nick Pitarra; colors: Michael Garland | |
| 16 | - | comic story | 20 | script: Ben Bates, Dustin Weaver; pencils: Ryan Browne, Sophie Campbell, Dustin Weaver, Ben Bates; inks: Ryan Browne, Sophie Campbell, Dustin Weaver, Ben Bates; colors: Bill Crabtree; letters: Shawn Lee | |
| 17 | Bebop & Rocksteady Destroy Everything #5 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Ryan Browne; inks: Ryan Browne; colors: Ryan Browne | |
| 18 | Teenage Mutant Ninja Turtles Universe #1 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Freddie Williams II | |
| 19 | The War to Come, Part 1 | comic story | 20 | script: Paul Allor; pencils: Damian Couceiro; inks: Damian Couceiro; colors: Ronda Pattison; letters: Shawn Lee | April O'Neil; Baxter Stockman; Donatello; John Bishop; Kara Lewis; Leonardo; Madame Null; Michelangelo; Raphael; Wesley Knight; Zodi |
| 20 | Teenage Mutant Ninja Turtles Universe #1 Damian Couceiro Variant Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 21 | Teenage Mutant Ninja Turtles Universe #2 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Freddie Williams II | |
| 22 | The War to Come, Part 2 | comic story | 20 | script: Paul Allor; pencils: Damian Couceiro; inks: Damian Couceiro; colors: Ronda Pattison; letters: Chris Mowry | Alex Winter; April O'Neil; Baxter Stockman; Donatello; John Bishop; Kara Lewis; Koya; Leonardo; Michelangelo; Raphael; Wesley Knight; Zodi |
| 23 | Teenage Mutant Ninja Turtles Universe #2 Damian Couceiro Variant Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 24 | Teenage Mutant Ninja Turtles Universe #3 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Freddie Williams II | |
| 25 | The War to Come, Part 3 | comic story | 20 | script: Paul Allor; pencils: Damian Couceiro; inks: Damian Couceiro; colors: Ronda Pattison; letters: Shawn Lee | Alex Winter; April O'Neil; Baxter Stockman; Donatello; Dragon; John Bishop; Kara Lewis; Leonardo; Michelangelo; Raphael; The Rat King; Wesley Knight; Zodi |
| 26 | Teenage Mutant Ninja Turtles Universe #3 Damian Couceiro Variant Cover | cover reprint (on interior page) | 1 | pencils: Damian Couceiro; inks: Damian Couceiro; colors: Damian Couceiro | |
| 27 | Teenage Mutant Ninja Turtles Universe #4 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Freddie Williams II | |
| 28 | The War to Come, Part 4 | comic story | 20 | script: Paul Allor; pencils: Damian Couceiro; inks: Damian Couceiro; colors: Ronda Pattison; letters: Shawn Lee | Alex Winter; April O'Neil; Baxter Stockman; Donatello; Harold Lilja; John Bishop; Kara Lewis; Leonardo; Madame Null; Metalhead; Michelangelo; Raphael; Wesley Knight; Zodi |
| 29 | Teenage Mutant Ninja Turtles Universe #1 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman; colors: Peter Laird | |
| 30 | Inside Out, Part 1 | comic story | 4 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Kevin Eastman, Bill Sienkiewicz; inks: Bill Sienkiewicz; colors: Tomi Varga; letters: Shawn Lee | Leonardo |
| 31 | Inside Out, Part 2 | comic story | 4 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Kevin Eastman, Bill Sienkiewicz; inks: Bill Sienkiewicz; colors: Tomi Varga; letters: Chris Mowry | Leonardo; Alopex; Koya |
| 32 | Inside Out, Part 3 | comic story | 4 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Kevin Eastman, Bill Sienkiewicz; inks: Bill Sienkiewicz; colors: Tomi Varga; letters: Shawn Lee | Leonardo; Dragon; Rat King |
| 33 | Inside Out, Part 4 | comic story | 4 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Kevin Eastman, Bill Sienkiewicz; inks: Bill Sienkiewicz; colors: Tomi Varga; letters: Shawn Lee | Leonardo; Harold Lilja; Metalhead; Fugitoid |
| 34 | Inside Out, Part 5 | comic story | 4 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Kevin Eastman, Bill Sienkiewicz; inks: Bill Sienkiewicz; colors: Tomi Varga; letters: Shawn Lee | Leonardo; April O'Neil; Casey Jones; Dark Leo; Tang Shen |
| 35 | Teenage Mutant Ninja Turtles Universe #2 Kevin Eastman Variant Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 36 | Teenage Mutant Ninja Turtles #65 Cover | cover reprint (on interior page) | 1 | pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: Mateus Santolouco | |
| 37 | Christmas Special | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz; pencils: Mateus Santolouco; inks: Mateus Santolouco; colors: Ronda Pattison; letters: Shawn Lee | Lindsey Baker; Angel Bridge; Woody Dirkins; Donatello; Casey Jones; Seymour Gutz; Herman; Leonardo; Man Ray; Michelangelo; Mondo Gecko; April O'Neil; Pepperoni; Pete; Sally Pride; Raphael; Slash; Agent Bishop; Splinter; Jimmy; Harold Lilja; Libby Meitner |
| 38 | Teenage Mutant Ninja Turtles #65 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Kevin Eastman; inks: Kevin Eastman | |
| 39 | Teenage Mutant Ninja Turtles Universe #5 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Freddie Williams II | |
| 40 | Urban Legends | comic story | 20 | script: Chris Mowry; pencils: Michael Dialynas; inks: Michael Dialynas; colors: Tomi Varga; letters: Shawn Lee | Old Hob; Hun; Leatherhead |
| 41 | Teenage Mutant Ninja Turtles Universe #5 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Michael Dialynas; inks: Michael Dialynas; colors: Michael Dialynas | |
| 42 | Teenage Mutant Ninja Turtles Universe #6 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Freddie Williams II | |
| 43 | The Rot in the Shell | comic story | 22 | script: Nick Pitarra, John Lees; pencils: Nick Pitarra; inks: Nick Pitarra; colors: Felipe Sobreiro; letters: Shawn Lee | Calvin Banks; Maureen Lin; Michelangelo; Wyrm; Donatello; Leonardo; Raphael; Splinter |
| 44 | Teenage Mutant Ninja Turtles Universe #6 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Nick Pitarra; inks: Nick Pitarra; colors: Felipe Sobreiro | |
| 45 | Teenage Mutant Ninja Turtles #66 Cover | cover reprint (on interior page) | 1 | pencils: Sophie Campbell; inks: Sophie Campbell; colors: Sophie Campbell | |
| 46 | Desperate Measures: Prologue | comic story | 20 | script: Kevin Eastman, Bobby Curnow, Tom Waltz, Sophie Campbell; pencils: Sophie Campbell; inks: Sophie Campbell; colors: Ronda Pattison; letters: Shawn Lee | Alopex; Angel Bridge; Kitsune; Raphael; Shredder |
| 47 | Teenage Mutant Ninja Turtles #66 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Sophie Campbell; inks: Sophie Campbell; colors: Sophie Campbell | |
| 48 | Teenage Mutant Ninja Turtles Universe #2 Antonio Fuso Variant Cover | cover reprint (on interior page) | 1 | pencils: Antonio Fuso; inks: Antonio Fuso; colors: Antonio Fuso | |
| 49 | Teenage Mutant Ninja Pepperoni | comic story | 4 | script: Sophie Campbell; pencils: Sophie Campbell; inks: Sophie Campbell; colors: Sophie Campbell; letters: Sophie Campbell | Alopex; Pepperoni; Raphael; Donatello; Leonardo; Michelangelo |
| 50 | Teenage Mutant Ninja Turtles Universe #3 Ryan Lee Variant Cover | cover reprint (on interior page) | 1 | pencils: Ryan Lee; inks: Ryan Lee; colors: Ryan Lee | |
| 51 | Teenage Mutant Ninja Turtles Universe #8 Hugo Petrus Variant Cover | cover reprint (on interior page) | 1 | pencils: Hugo Petrus; inks: Hugo Petrus; colors: Hugo Petrus | |
| 52 | What is Ninja?, Part 1 | comic story | 4 | script: Brahm Revel; pencils: Brahm Revel; inks: Brahm Revel; colors: Brahm Revel; letters: Shawn Lee | Jennika; Raphael |
| 53 | What is Ninja?, Part 2 | comic story | 4 | script: Brahm Revel; pencils: Brahm Revel; inks: Brahm Revel; colors: Brahm Revel; letters: Shawn Lee, Chris Mowry | Donatello; Jennika; Ivan; Metalhead |
| 54 | What is Ninja?, Part 3 | comic story | 4 | script: Brahm Revel; pencils: Brahm Revel; inks: Brahm Revel; colors: Brahm Revel; letters: Shawn Lee | Jennika; Michelangelo |
| 55 | What is Ninja?, part 4 | comic story | 4 | script: Brahm Revel; pencils: Brahm Revel; inks: Brahm Revel; colors: Brahm Revel; letters: Shawn Lee | Jennika; Leonardo; Splinter; Shredder |
| 56 | Teenage Mutant Ninja Turtles Universe #6 Logan Faerber Variant Cover | cover reprint (on interior page) | 1 | pencils: Logan Faerber; inks: Logan Faerber; colors: Logan Faerber | |
| 57 | Teenage Mutant Ninja Turtles Universe #7 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Freddie Williams II | |
| 58 | Metalhead 2.0, Part 1 | comic story | 20 | script: Ryan Ferrier; pencils: Adam Gorham; inks: Adam Gorham; colors: Ronda Pattison; letters: Shawn Lee, Chris Mowry | Donatello; Leonardo; Metalhead; Michelangelo; Raphael |
| 59 | Teenage Mutant Ninja Turtles Universe #7 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Adam Gorham; inks: Adam Gorham; colors: Adam Gorham | |
| 60 | Teenage Mutant Ninja Turtles Universe #8 Cover | cover reprint (on interior page) | 1 | pencils: Freddie Williams II; inks: Freddie Williams II; colors: Freddie Williams II | |
| 61 | Metalhead 2.0, Part 2 | comic story | 20 | script: Ryan Ferrier; pencils: Adam Gorham; inks: Adam Gorham, Joshua Hixson; colors: Ronda Pattison; letters: Shawn Lee | Donatello; Leonardo; Metalhead; Michelangelo; Raphael |
| 62 | Teenage Mutant Ninja Turtles Universe #8 Subscription Cover | cover reprint (on interior page) | 1 | pencils: Adam Gorham; inks: Adam Gorham; colors: Adam Gorham | |
| 63 | - | illustration | 1 | letters: typeset | |