| 0 | - | cover | 1 | pencils: Stan Sakai; inks: Stan Sakai | Miyamoto Usagi |
| 2 | Usagi Yojimbo Book Three | credits, title page | 1 | | |
| 4 | Usagi Yojimbo Book Three | credits, title page | 3 | pencils: Stan Sakai; inks: Stan Sakai | Miyamoto Usagi |
| 6 | Introduction | foreword, introduction, preface, afterword | 1 | script: Robert L. Asprin | |
| 8 | Chapter One: The Tower | credits, title page | 1 | pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | |
| 10 | The Tower | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 11 | Chapter Two: A Mother's Love | credits, title page | 1 | pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | |
| 13 | A Mother's Love | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 14 | Chapter Three: Return of the Blind Swordspig | credits, title page | 1 | pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | |
| 16 | Return of the Blind Swordspig | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi, Zato-Ino |
| 17 | Chapter Four: Blade of the Gods | credits, title page | 1 | pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | |
| 19 | Blade of the Gods | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jei, Miyamoto Usagi |
| 20 | Chapter Five: The Tea Cup | credits, title page | 1 | pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | |
| 22 | The Tea Cup | comic story | 20 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Groo, Miyamoto Usagi |
| 23 | Chapter Six: The Shogun's Gift | credits, title page | 1 | pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | |
| 25 | The Shogun's Gift | comic story | 22 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi, Lord Noriyuki, Tomoe Ame |
| 26 | Epilogue: Turtle Soup and Rabbit Stew | credits, title page | 1 | pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Usagi Yojimbo [Miyamoto Usagi]; Leonardo |
| 27 | - | foreword, introduction, preface, afterword | 1 | script: Stan Sakai | |
| 28 | Turtle Soup and Rabbit Stew | comic story | 6 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Donatello, Leonardo, Michelangelo, Miyamoto Usagi, Raphael |
| 30 | The Usagi Library | promo (ad from the publisher) | 1 | letters: typeset | |
| 31 | - | promo (ad from the publisher) | 1 | pencils: Stan Sakai; inks: Stan Sakai | Miyamoto Usagi |