| 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 | The Sound of One Pen Drawing | foreword, introduction, preface, afterword | 1 | script: Walter Simonson; pencils: Walter Simonson; inks: Walter Simonson | |
| 6 | Traitors of the Earth, Part One | comic story | 25 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Kitsune, Miyamoto Usagi, Sasuké |
| 7 | Traitors of the Earth, Part Two | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Kitsune, Miyamoto Usagi, Sasuké |
| 8 | Traitors of the Earth, Part Three | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Kitsune, Miyamoto Usagi, Sasuké |
| 9 | What the Little Thief Heard | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Kitsune, Miyamoto Usagi |
| 10 | One Dark and Stormy Night | comic story | 6 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; letters: Stan Sakai | Miyamoto Usagi |
| 11 | The Hidden Fortress | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 12 | A Place to Stay | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 13 | The Death of Lord Hikiji | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 14 | Introduction | foreword, introduction, preface, afterword | 2 | script: Geof Darrow; pencils: Geof Darrow; inks: Geof Darrow | |
| 15 | A Town Called Hell, Part 1 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 16 | A Town Called Hell, Part 2 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 17 | Nukekubi | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 18 | The Sword of Narukami | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 19 | Teru Teru Bozu | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Jei, Keiko, Miyamoto Usagi |
| 20 | Encounter at Blood Tree Pass | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 21 | Return to Hell, Part One | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 22 | Return to Hell, Part Two | comic story | 25 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 23 | Introduction | foreword, introduction, preface, afterword | 1 | script: George Takei | |
| 24 | Taiko, Part One | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 25 | Taiko, Part Two | comic story | 25 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 26 | Toad Oil | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Kitsune, Miyamoto Usagi |
| 27 | The Return of the Lord of Owls | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 28 | Those Who Tread on the Scorpion's Tail, Part One | comic story | 28 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 29 | Those Who Tread on the Scorpion's Tail, Part 2 | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 30 | Those Who Tread on the Scorpion's Tail, Part Three | comic story | 24 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; letters: Stan Sakai | Miyamoto Usagi |
| 31 | Cut the Plum | comic story | 2 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth; letters: Stan Sakai | Jotaro, Miyamoto Usagi |
| 32 | Story Notes | text article | 5 | script: Stan Sakai; pencils: Stan Sakai; inks: Stan Sakai | |
| 33 | Usagi Yojimbo Volume Three #117 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Kitsune, Miyamoto Usagi |
| 34 | Usagi Yojimbo Volume Three #118 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Kitsune, Miyamoto Usagi |
| 35 | Usagi Yojimbo Volume Three #119 | cover reprint (on interior page) | 2 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 36 | Usagi Yojimbo Volume Three #120 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Kitsune, Miyamoto Usagi |
| 37 | Usagi Yojimbo Volume Three #121 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 38 | Usagi Yojimbo Volume Three #122 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 39 | Usagi Yojimbo Volume Three #123 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 40 | Usagi Yojimbo Volume Three #123, Dark Horse 100 Special Edition Variant Cover | cover reprint (on interior page) | 2 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Murakami Gennosuke, Miyamoto Usagi |
| 41 | Usagi Yojimbo Volume Three #124 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 42 | Usagi Yojimbo Volume Three #125 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 43 | Usagi Yojimbo Volume Three #126 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 44 | Usagi Yojimbo Volume Three #127 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 45 | Usagi Yojimbo Volume Three #128 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 46 | Usagi Yojimbo Volume Three #129 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 47 | Usagi Yojimbo Volume Three #130 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 48 | Usagi Yojimbo Volume Three #131 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 49 | Usagi Yojimbo Volume Three #132 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 50 | Usagi Yojimbo Volume Three #133 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 51 | Usagi Yojimbo Volume Three #134 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 52 | Usagi Yojimbo Volume Three #135 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 53 | Usagi Yojimbo Volume Three #136 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 54 | Usagi Yojimbo Volume Three #136, Dark Horse 25th Anniversary Variant Cover | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 55 | Usagi Yojimbo Volume Three #137 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 56 | Usagi Yojimbo Volume Three #138 | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Miyamoto Usagi |
| 57 | Usagi Yojimbo Book 26: Traitors of the Earth | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Miyamoto Usagi |
| 58 | Usagi Yojimbo Book 27: A Town Called Hell | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Miyamoto Usagi |
| 59 | Usagi Yojimbo Book 28: Red Scorpion | cover reprint (on interior page) | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Miyamoto Usagi |
| 60 | Extras | illustration | 1 | pencils: Stan Sakai, Stan Lee | |
| 61 | 25th Anniversary Poster | illustration | 2 | pencils: Stan Sakai; inks: Stan Sakai; colors: Tom Luth | Chizu, Murakami Gennosuke, Inspector Ishida, Jotaro, Katsuichi, Kitsune, Miyamoto Usagi, Lord Noriyuki, Sasuké, Tomoe Ame |
| 62 | 2009 San Diego Comic-Con | illustration | 1 | pencils: Stan Sakai; inks: Stan Sakai; colors: Stan Sakai | Jotaro, Miyamoto Usagi |
| 63 | Pinup | illustration | 1 | pencils: Chris Houghton; inks: Chris Houghton | Miyamoto Usagi |