| 1 | Title |
| 2 | File Select |
| 3 | Prologue |
| 4 | Prologue - A Young Boy Dressed In Green |
| 5 | Prologue - A Beautiful Princess |
| 6 | Prologue - The Evil King |
| 7 | Prologue - A True Hero |
| 8 | Prologue - A Happy Pirate Ending! |
| 9 | Tetra's Pirates |
| 10 | The Ghost Ship Appears |
| 11 | Tetra Boards The Ghost Ship |
| 12 | Link!!! Save Me!!!!! |
| 13 | Mercay Island |
| 14 | House |
| 15 | Oshus' Theme |
| 16 | Small Item Get |
| 17 | Mysterious Cave |
| 18 | Danger! Monsters Ahead! |
| 19 | Item Get |
| 20 | Sword Training - Targeted Attack |
| 21 | Sword Training A |
| 22 | Sword Training B |
| 23 | Sword Training C |
| 24 | Targeted Attack Perfected |
| 25 | Sword Training - Side Slash |
| 26 | Sword Training D |
| 27 | Side Slash Perfected |
| 28 | Sword Training - Spin Attack |
| 29 | Sword Training E |
| 30 | Spin Attack Perfected |
| 31 | Dungeon |
| 32 | You Got....! Nothing... |
| 33 | Linebeck's Theme |
| 34 | Item Get (Dizzy) |
| 35 | Linebeck's Theme (No Intro) |
| 36 | Ocean |
| 37 | Beedle's Shop Ship |
| 38 | Astrid's House |
| 39 | Battle |
| 40 | Fortune Telling |
| 41 | Boss Battle |
| 42 | Spirit Freed |
| 43 | Spirit Joins |
| 44 | Heart Container Get |
| 45 | Spirit Item Get |
| 46 | Phantom Hourglass Get |
| 47 | The Phantom Hourglass |
| 48 | Phantoms In Pursuit |
| 49 | A Fatal Mistake |
| 50 | Game Over |
| 51 | The Ghost Ship |
| 52 | Navigating the Fog |
| 53 | Sand of Hours |
| 54 | Sand of Hours Get |
| 55 | Salvatore's Cannon Game |
| 56 | Salvage Catch |
| 57 | Miss! |
| 58 | Maritime Battle |
| 59 | Spirit of Courage Get |
| 60 | Oshus' Story |
| 61 | Ciela, The Spirit of Courage |
| 62 | The She-Pirate, Jolene |
| 63 | Rupoor Get |
| 64 | Tetra Discovered |
| 65 | The Life Leech, Bellum |
| 66 | Tetra!!!!! |
| 67 | Linebeck Leaps Into Action |
| 68 | Freedle's Song |
| 69 | The She-Pirate, Jolene (No Intro) |
| 70 | Goron Island |
| 71 | Goron House |
| 72 | Question Two Correct |
| 73 | Question Three Correct |
| 74 | Question Four Correct |
| 75 | Question Five Correct |
| 76 | Drum Roll |
| 77 | Goron Initiation Success |
| 78 | Big Gold Rupee Get |
| 79 | Oshus' Story (No Intro) |
| 80 | Phantom Sword Get |
| 81 | Bellum Battle |
| 82 | Ciela's Memory Released |
| 83 | Bellum Battle (No Intro) |
| 84 | Time Stopped |
| 85 | Tetra Restored |
| 86 | Tetra's Theme |
| 87 | A Happy Ending Postponed |
| 88 | Bellum's Theme |
| 89 | Ghost Ship Battle |
| 90 | Bellum's Theme (Intro - Grandpa!) |
| 91 | Wake Up, Link! |
| 92 | Linebeck's Struggle |
| 93 | Linebeck Possessed |
| 94 | Phantom Linebeck Battle |
| 95 | The Ocean King |
| 96 | Ocean King's Theme |
| 97 | Ciela's Parting Words |
| 98 | Good-Bye |
| 99 | Staff Roll |
| 100 | The End |
| 101 | Turn Start |
| 102 | Battle Mode (Link) |
| 103 | Link Felled |
| 104 | Opponent Link Felled |
| 105 | Win |
| 106 | Lose (Or Draw) |
| 107 | Results |
| 108 | Multiplayer - Stage Select (Salvatore's Cannon Game Double) |
| 109 | Goron Quiz Fail (Miss! Double) |
| 110 | Minigame (Sword Training A Double) |
| 111 | Targeted Attack Perfected (Unused Tiny Version) |
| 112 | Miss! Double 2 |
| 113 | Freedle - Guitar Strum 1 |
| 114 | Freedle - Guitar Strum 2 |
| 115 | Freedle - Guitar Strum 3 |
| 116 | Freedle - Guitar Strum 4 |
| 117 | Freedle - Guitar Strum 5 |
| 118 | Freedle - Guitar Strum 6 |
| 119 | Freedle - Guitar Strum 7 |
| 120 | Freedle - Guitar Strum 8 |
| 121 | Freedle - Guitar Strum 9 |
