| 0 | - | cover | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Miyamoto Usagi |
| 1 | Inside fron Cover | blank page(s) | 1 | | |
| 2 | Half Title Page | credits, title page | 1 | letters: typeset | |
| 3 | Full Title Page | credits, title page | 2 | pencils: Stan Sakai; inks: Stan Sakai | Miyamoto Usagi |
| 4 | Copyright Page | statement of ownership | 1 | letters: typeset | |
| 5 | Dedication Page | foreword, introduction, preface, afterword | 1 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai | |
| 6 | Contents | table of contents | 2 | pencils: Stan Sakai; inks: Stan Sakai | |
| 7 | Foreword | foreword, introduction, preface, afterword | 2 | script: Jamie S. Rich | |
| 8 | Cast of Characters | character profile | 1 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai | |
| 9 | Origin Tale | comic story | 4 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Jamie S. Rich | |
| 10 | Shades of Death | credits, title page | 1 | letters: typeset | |
| 11 | Storytelling from a Master | foreword, introduction, preface, afterword | 1 | script: William Stout | |
| 12 | Shades of Green (Chapter 1) | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Donatello, Murakami Gennosuke, Leonardo, Michelangelo, Miyamoto Usagi, Raphael |
| 13 | Shades of Green Chapter 2 | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Donatello, Murakami Gennosuke, Leonardo, Michelangelo, Miyamoto Usagi, Raphael |
| 14 | Shades of Green Chapter 3 | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Donatello, Murakami Gennosuke, Leonardo, Michelangelo, Miyamoto Usagi, Raphael |
| 15 | Jizo | comic story | 8 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 16 | Usagi's Garden | comic story | 8 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Katsuichi, Miyamoto Usagi |
| 17 | Autumn | comic story | 8 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Katsuichi, Miyamoto Usagi |
| 18 | Shi (Part 1) | comic story | 28 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 19 | Shi Part 2 | comic story | 28 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 20 | The Lizard's Tale | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 21 | Battlefield Part 1 | comic story | 8 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Katsuichi, Miyamoto Usagi |
| 22 | Battlefield Part 2 | comic story | 10 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Katsuichi, Miyamoto Usagi |
| 23 | Battlefield Part 3 | comic story | 8 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Katsuichi, Miyamoto Usagi |
| 24 | Daisho | credits, title page | 1 | letters: typeset | |
| 25 | Classic Storytelling | foreword, introduction, preface, afterword | 2 | script: James Robinson | |
| 26 | Blank | blank page(s) | 1 | letters: typeset | |
| 27 | The Music of Heaven | comic story | 18 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 28 | The Gambler, the Widow, and the Ronin | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 29 | The Nature of the Viper | comic story | 7 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Jei |
| 30 | Blank | blank page(s) | 1 | letters: typeset | |
| 31 | Slavers (Part 1) | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 32 | Slavers Part 2 | comic story | 21 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 33 | Blank | recap | 1 | letters: typeset | |
| 34 | Daisho (Part 1) | comic story | 21 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Miyamoto Usagi |
| 35 | Mongrels | comic story | 7 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Murakami Gennosuke |
| 36 | Daisho Part 2 | comic story | 28 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Murakami Gennosuke, Miyamoto Usagi |
| 37 | Runaways (Part 1) | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Murakami Gennosuke, Miyamoto Usagi |
| 38 | Runaways Part 2 | comic story | 28 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 39 | The Brink of Life and Death | credits, title page | 1 | letters: typeset | |
| 40 | Discoveries | foreword, introduction, preface, afterword | 2 | script: Kurt Busiek | |
| 41 | Blank | blank page(s) | 1 | letters: typeset | |
| 42 | Black Soul | comic story | 8 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | Jei |
| 43 | Kaiso | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 44 | A Meeting of Strangers | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Michael Dooney | |
| 45 | Noodles (Part 1) | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Jamie S. Rich | Kitsune, Miyamoto Usagi |
| 46 | Noodles part 2 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Jamie S. Rich | Kitsune, Miyamoto Usagi |
| 47 | The Wrath Of The Tangled Skein | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Jamie S. Rich | |
| 48 | The Bonze's Story | comic story | 4 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Jamie S. Rich | |
| 49 | Bats, the Cat, and the Rabbit | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Jamie S. Rich | Chizu, Miyamoto Usagi |
| 50 | The Chrysanthemum Pass | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Jamie S. Rich | |
| 51 | Lightning Strikes Twice | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai; editing: Jamie S. Rich | Miyamoto Usagi |
| 52 | - | blank page(s) | 1 | | |
| 53 | Story Notes | text article | 8 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Michael Dooney | |
| 54 | - | blank page(s) | 1 | | |
| 55 | Gallery: Usagi Yojimbo Volume Two #1 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Michael Dooney | |
| 56 | Gallery: Usagi Yojimbo Volume Two #2 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Michael Dooney | |
| 57 | Gallery: Usagi Yojimbo Volume Two #3 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Michael Dooney | |
| 58 | Gallery: Usagi Yojimbo Volume Two #4 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Michael Dooney | |
| 59 | Gallery: Usagi Yojimbo Volume Two #5 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Michael Dooney | |
| 60 | Gallery: Usagi Yojimbo Volume Two #6 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Michael Dooney | |
| 61 | Gallery: Usagi Yojimbo Volume Two #7 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Michael Dooney | |
| 62 | Gallery: Usagi Yojimbo Volume Two #8 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 63 | Gallery: Usagi Yojimbo Volume Two #9 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 64 | Gallery: Usagi Yojimbo Volume Two #10 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 65 | Gallery: Usagi Yojimbo Volume Two #11 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 66 | Gallery: Usagi Yojimbo Volume Two #12 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 67 | Gallery: Usagi Yojimbo Volume Two #13 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 68 | Gallery: Usagi Yojimbo Volume Two #14 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 69 | Gallery: Usagi Yojimbo Volume Two #15 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 70 | Gallery: Usagi Yojimbo Volume Two #16 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Michael Dooney | |
| 71 | Gallery: Usagi Yojimbo Volume Three #1 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Jamie S. Rich | Miyamoto Usagi |
| 72 | Gallery: Usagi Yojimbo Volume Three #2 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Jamie S. Rich | |
| 73 | Gallery: Usagi Yojimbo Volume Three #3 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Jamie S. Rich | |
| 74 | Gallery: Usagi Yojimbo Volume Three #4 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Jamie S. Rich | |
| 75 | Gallery: Usagi Yojimbo Volume Three #5 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; editing: Jamie S. Rich | |
| 76 | Gallery: Usagi Yojimbo Volume Three #6 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Jamie S. Rich | |
| 77 | Gallery: Usagi Yojimbo Book 8: Shades of Death | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Jamie S. Rich | |
| 78 | Gallery: Usagi Yojimbo Book 9: Daisho | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Jamie S. Rich | |
| 79 | Gallery: Usagi Yojimbo Book 10: The Brink of Life and Death | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai; editing: Jamie S. Rich | |
| 80 | Cover Sketches | illustration | 4 | pencils: Stan Sakai; inks: Stan Sakai; editing: Jamie S. Rich | |
| 81 | About the Author | text article | 1 | editing: Jamie S. Rich | |
| 82 | Usagi Yojimbo | promo (ad from the publisher) | 1 | pencils: Stan Sakai; inks: Stan Sakai; editing: Jamie S. Rich | |
| 83 | Dark Horse Comics, Inc. | credits, title page | 1 | pencils: Stan Sakai; inks: Stan Sakai; editing: Jamie S. Rich | |
| 84 | Inside Back Cover | blank page(s) | 1 | | |
| 85 | Back Cover | text article | 1 | letters: typeset | |