| 0 | - | cover | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 1 | Title Page and Credits | credits, title page | 4 | pencils: Stan Sakai; inks: Stan Sakai | |
| 2 | Dedication | foreword, introduction, preface, afterword | 1 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai | |
| 3 | Contents | table of contents | 2 | pencils: Stan Sakai; inks: Stan Sakai | |
| 4 | Cast of Characters | character profile | 1 | pencils: Stan Sakai; inks: Stan Sakai | |
| 5 | Introduction | foreword, introduction, preface, afterword | 1 | script: Brian K. Vaughan | |
| 6 | Ninja Hunt | comic story | 1 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 7 | Shizukiri | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 8 | Boss Hamanaka's Fortune, Part One | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 9 | Boss Hamanaka's Fortune, Part Two | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 10 | Rain and Thunder | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Jei, Keiko |
| 11 | Bridge of Tears | comic story | 25 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 12 | Fever Dream | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Chizu, Jei, Miyamoto Usagi, Lord Noriyuki, Tomoe Ame |
| 13 | The Killer | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 14 | Introduction | foreword, introduction, preface, afterword | 1 | script: Charles Solomon | |
| 15 | The Darkness and the Soul, Part 1 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jizonobu-Sensei; Kin-Sensei; Lord Goyo; Lord Goyo's daughter; Jubei; Jubei's mother; Ibaraki the Dark Priest |
| 16 | The Darkness and the Soul, Part 2 | comic story | 25 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jei |
| 17 | Sparrows, Chapter 1 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Jei, Keiko, Miyamoto Usagi |
| 18 | Sparrows, Chapter Two | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Jei, Keiko, Miyamoto Usagi |
| 19 | Sparrows Chapter 3 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Jei, Keiko, Miyamoto Usagi |
| 20 | Sparrows Chapter 4 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Jei, Miyamoto Usagi |
| 21 | Sparrows Chapter 5 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Jei, Miyamoto Usagi |
| 22 | My Journey with Usagi Yojimbo | foreword, introduction, preface, afterword | 1 | script: Floyd Norman | |
| 23 | Kitsune Gari | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Miyamoto Usagi |
| 24 | Sakura Part One | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Miyamoto Usagi |
| 25 | Sakura Part Two | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Miyamoto Usagi |
| 26 | Snitch | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke, Miyamoto Usagi |
| 27 | The Beggar | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 28 | The Fortress | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Chizu, Miyamoto Usagi |
| 29 | The Outlaw | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Murakami Gennosuke |
| 30 | Saya | comic story | 8 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; letters: Stan Sakai | Miyamoto Usagi |
| 31 | Story Notes | text article | 1 | script: Stan Sakai | |
| 32 | Usagi Yojimbo Volume Three #95 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 33 | Usagi Yojimbo Volume Three #96 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 34 | Usagi Yojimbo Volume Three #97 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi; Kin; Jodo "Baka" Hamanaka |
| 35 | Usagi Yojimbo Volume Three #98 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke |
| 36 | Usagi Yojimbo Volume Three #99 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 37 | Usagi Yojimbo Volume Three #100 | cover reprint (on interior page) | 2 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke, Jotaro, Miyamoto Usagi, Tomoe Ame |
| 38 | Usagi Yojimbo Volume Three #101 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jei, Miyamoto Usagi |
| 39 | Usagi Yojimbo Volume Three #102 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 40 | Usagi Yojimbo Volume Three #103 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 41 | Usagi Yojimbo Volume Three #104 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 42 | Usagi Yojimbo Volume Three #105 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 43 | Usagi Yojimbo Volume Three #106 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke, Miyamoto Usagi |
| 44 | Usagi Yojimbo Volume Three #107 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke, Jei, Miyamoto Usagi |
| 45 | Usagi Yojimbo Volume Three #108 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Jei, Miyamoto Usagi |
| 46 | Usagi Yojimbo Volume Three #109 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke, Miyamoto Usagi |
| 47 | Usagi Yojimbo Volume Three #110 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke, Miyamoto Usagi |
| 48 | Usagi Yojimbo Volume Three #111 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 49 | Usagi Yojimbo Volume Three #112 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke, Miyamoto Usagi |
| 50 | Usagi Yojimbo Volume Three #113 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke, Miyamoto Usagi |
| 51 | Usagi Yojimbo Volume Three #114 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 52 | Usagi Yojimbo Volume Three #115 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 53 | Usagi Yojimbo Volume Three #116 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 54 | Usagi Yojimbo Book 23: Bridge of Tears | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Miyamoto Usagi |
| 55 | Usagi Yojimbo Book 24: Return of the Black Soul | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Miyamoto Usagi |
| 56 | Usagi Yojimbo Book 25: Fox Hunt | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Miyamoto Usagi |
| 57 | Groo vs. Usagi: Who Would Win? | comic story | 1 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Groo, Miyamoto Usagi |
| 58 | The Day of the Shadow | comic story | 1 | script: Stephane Heude; pencils: Laurent de Andrade; inks: Laurent de Andrade | Miyamoto Usagi |
| 59 | The Stan Sakai Celebrity Roast, Part 1 | comic story | 6 | script: Mike Richardson; pencils: Rick Geary; inks: Rick Geary; letters: Rick Geary | Mike Richardson; Stan Sakai; Diana Schutz; Concrete; The Mask; Rick Geary |
| 60 | The Stan Sakai Celebrity Roast, Part 2 | comic story | 1 | script: Frank Miller; pencils: Frank Miller; inks: Frank Miller; letters: Frank Miller | Miyamoto Usagi |
| 61 | The Stan Sakai Celebrity Roast, Part 3 | comic story | 1 | script: Diana Schutz; pencils: Matt Wagner; inks: Matt Wagner; letters: Tom Orzechowski | Concrete, Miyamoto Usagi |
| 62 | The Stan Sakai Celebrity Roast, Part 4 | comic story | 2 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Stan Sakai; Sergio Aragones |
| 63 | The Stan Sakai Celebrity Roast, Part 5 | comic story | 4 | script: Sergio Aragonés; pencils: Sergio Aragonés; inks: Sergio Aragonés; letters: Stan Sakai | Miyamoto Usagi |
| 64 | The Stan Sakai Celebrity Roast, Part 6 | comic story | 2 | script: Jamie S. Rich; pencils: Andi Watson; inks: Andi Watson; letters: Andi Watson | Miyamoto Usagi |
| 65 | The Stan Sakai Celebrity Roast, Part 7 | comic story | 1 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Stan Sakai |
| 66 | The Stan Sakai Celebrity Roast, Part 8 | comic story | 1 | script: Jeff Smith; pencils: Jeff Smith; inks: Jeff Smith; letters: Jeff Smith | Jeff Smith; Stan Sakai; unnamed comic convention guests |
| 67 | The Stan Sakai Celebrity Roast, Part 9 | comic story | 4 | script: Mark Evanier; pencils: Scott Shaw!; inks: Scott Shaw!; letters: Scott Shaw! | Captain Carrot, Roger Rodney Rabbit |
| 68 | The Stan Sakai Celebrity Roast, Part 10 | comic story | 2 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Stan Sakai; Guy Davis |
| 69 | The Stan Sakai Celebrity Roast, Part 11 | comic story | 2 | script: Guy Davis; pencils: Guy Davis; inks: Guy Davis | Miyamoto Usagi |
| 70 | The Stan Sakai Celebrity Roast, Part 12 | comic story | 4 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Chizu, Murakami Gennosuke, Jotaro, Miyamoto Usagi, Lord Noriyuki, Tomoe Ame |
| 71 | Usagi Yojimbo #99 Alternate Ending | comic story | 1 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |