| 1 | Opening ~ Title Screen |
| 2 | File Select |
| 3 | Prologue |
| 4 | After the Prologue |
| 5 | Aboda Village |
| 6 | Final Exam |
| 7 | Castle Town |
| 8 | Got an Item! |
| 9 | Got a Small Item! |
| 10 | Hyrule Castle |
| 11 | The Ceremony Begins |
| 12 | Zelda Appears |
| 13 | Zelda's Lullaby |
| 14 | Chancellor Cole's Smirk |
| 15 | Dumbfounded Link |
| 16 | Zelda and the Spirit Flute |
| 17 | Got the Recruit Uniform! |
| 18 | Sneaking out of the Castle |
| 19 | Spirit Tracks Disappearing |
| 20 | Tower of Spirits Destroyed |
| 21 | The Demon Train |
| 22 | Chancellor Cole |
| 23 | Cole Shock Chord A (Your) |
| 24 | Cole Shock Chord B (High) |
| 25 | Cole Shock Chord C (ness!) |
| 26 | Battle Preparations |
| 27 | Alfonzo vs. Byrne |
| 28 | Zelda's Body Stolen! |
| 29 | Zelda Taken Away |
| 30 | Ownerless Hyrule Castle |
| 31 | Zelda's Spirit |
| 32 | The Spirit Flute |
| 33 | Let's Go, Link! |
| 34 | Sword Lesson 1 |
| 35 | Sword Training A |
| 36 | Sword Lesson 2 |
| 37 | Sword Training B |
| 38 | Sword Lesson 3 |
| 39 | Sword Training C |
| 40 | In the Fields |
| 41 | Cave |
| 42 | Rats! |
| 43 | The Ominous Broken Tower |
| 44 | Meeting Anjean |
| 45 | Zelda Loses It |
| 46 | Hysterical Zelda |
| 47 | Tower of Spirits |
| 48 | Tower of Spirits -Dungeon- |
| 49 | A Phantom Appears |
| 50 | Spotted! (Phantoms) |
| 51 | A Fatal Mistake |
| 52 | Watch Out, Link! |
| 53 | Zelda Possesses a Phantom |
| 54 | Zelda Ready to Fight! |
| 55 | Got the Rail Map! |
| 56 | The Spirit Tracks Reappear |
| 57 | Select Rail Route |
| 58 | Overworld Adventure |
| 59 | Battle on the Tracks! |
| 60 | Whittleton |
| 61 | The Lost Woods |
| 62 | Discovery |
| 63 | Sound Stone of Awakening |
| 64 | Spirit Flute Practice - Awakening |
| 65 | Song of Awakening |
| 66 | Song of Awakening (Short) |
| 67 | Learned Music |
| 68 | Sanctuary |
| 69 | Lokomo Song Practice - Gage |
| 70 | Gage Duet |
| 71 | Sound Stone of Healing |
| 72 | Spirit Flute Practice - Healing |
| 73 | Song of Healing |
| 74 | Song of Healing (Short) |
| 75 | Forest, Snow and Ocean Temple |
| 76 | Dungeon Gauntlet |
| 77 | Mini-Boss |
| 78 | Got a Treasure! |
| 79 | Spotted! (Key Master) |
| 80 | Stagnox, Armored Colossus |
| 81 | Boss Defeated |
| 82 | The Force Gem Awakens |
| 83 | Power Across the Spirit Tracks |
| 84 | Restoring the Tower of Spirits (Partial) |
| 85 | Got a Heart Container! |
| 86 | Dark Trains Approaching |
| 87 | Game Over |
| 88 | Got a Spirit Train Car! |
| 89 | Catching a Rabbit |
| 90 | Miss! |
| 91 | Cursed Overworld |
| 92 | Anouki Village in the Dark |
| 93 | Sound Stone of Discovery |
| 94 | Spirit Flute Practice |
| 95 | Song of Discovery |
| 96 | Song of Discovery (Short) |
| 97 | The Great Eye in the Dark |
| 98 | Rocktite Closing |
| 99 | Lokomo Song Practice - Steem |
| 100 | Steem Duet |
| 101 | The Blizzard |
| 102 | Fraaz, Master of Icy Fire |
| 103 | Anouki Village |
| 104 | Beedle's Air Shop |
| 105 | Sword Training D |
| 106 | Linebeck III Enters |
| 107 | Linebeck III |
| 108 | Sound Stone of Light |
| 109 | Spirit Flute Practice - Light |
| 110 | Song of Light |
| 111 | Song of Light (Short) |
| 112 | Papuchia Village |
| 113 | The Wise One |
| 114 | The Future Revealed |
| 115 | Sound Stone of Birds |
| 116 | Spirit Flute Practice - Birds |
| 117 | Song of Birds |
| 118 | Song of Birds (Short) |
| 119 | Pirate Attack! |
| 120 | Got a Force Gem! |
| 121 | Lokomo Song Practice - Carben |
| 122 | Carben Duet |
| 123 | Underwater |
| 124 | Phytops, Barbed Menace |
| 125 | Tank and Bomb Ship Attack |
| 126 | Whip Race |
| 127 | Byrne |
| 128 | Anjean's Decision |
| 129 | Goron Village in Lava Spouts |
| 130 | Out of Cargo |
| 131 | Lokomo Song Practice - Embrose |
| 132 | Embrose Duet |
| 133 | Snuglars |
| 134 | Fire and Sand Temple |
| 135 | Cragma, Lava Lord |
| 136 | Restoring the Tower of Spirits (Complete) |
| 137 | Goron Village |
| 138 | Goron Target Range - Blue Target |
| 139 | Goron Target Range - Red Target (One) |
| 140 | Goron Target Range - Red Target (Two) |
| 141 | Goron Target Range - Red Target (Three) |
| 142 | Goron Target Range - Goron Target |
| 143 | Tower of Spirits Staircase (First Level) |
| 144 | Tower of Spirits Staircase (Second Level) |
| 145 | Tower of Spirits Staircase (Third Level) |
| 146 | Tower of Spirits Staircase (Fourth Level) |
| 147 | Tower of Spirits Staircase (Full Version) |
| 148 | Fight Against Byrne |
| 149 | Link and Zelda's Friendship |
| 150 | Resurrection of the Demon King |
| 151 | Fleeing by Demon Train |
| 152 | Anjean Devises a Plan |
| 153 | Lokomo Song Practice - Rael |
| 154 | Rael Duet |
| 155 | Skeldritch, Ancient Demon |
| 156 | Zelda’s Dashed Hopes |
| 157 | Byrne Awakes |
| 158 | Got the Lokomo Sword! |
| 159 | Lost at Sea Station |
| 160 | Dark Link |
| 161 | The Dark Realm |
| 162 | Tears of Light in the Dark Realm |
| 163 | Facing the Demon Train |
| 164 | Before the Final Battle |
| 165 | The Chancellor's Annoyance |
| 166 | The Chancellor's Limit |
| 167 | The Revival's Completion |
| 168 | Fighting Cole and Malladus |
| 169 | Malladus Weakened |
| 170 | Bodiless Malladus |
| 171 | The Unenterable Body |
| 172 | Byrne Comes to the Rescue |
| 173 | Link Catches Zelda |
| 174 | Byrne's Death |
| 175 | The End of the Chancellor |
| 176 | Malladus's Transformation |
| 177 | Malladus in Cole’s Body |
| 178 | Final Battle ~ Protecting Zelda |
| 179 | The Sacred Duet |
| 180 | Final Battle ~ Malladus |
| 181 | Final Battle ~ Malladus (with Duet) |
| 182 | Saying Goodbye |
| 183 | The Lokomos Ascend |
| 184 | Staff Roll |
| 185 | The End |
| 186 | Battle Mode |
| 187 | Get Ready |
| 188 | Ready, Set, Battle! |
| 189 | A Phantom Appears (Battle Mode) |
| 190 | Spotted! (Battle Mode) |
| 191 | Invincibility |
| 192 | Battle Mode Results |
| 193 | Tag Mode |
| 194 | Got a Treasure! Double |
| 195 | Miss! Double |
| 196 | Cragma, Lava Lord (Retry) |
| 197 | Fraaz, Master of Icy Fire (Retry) |
| 198 | Passenger - Mood Down |
| 199 | Passenger - Mood Up |
| 200 | Passenger - Mood Very Low |
| 201 | Spirit Zelda Appears |
| 202 | Spirit Zelda Disappears |
| 203 | Stagnox and Phytops (Retry) |
| 204 | Tag Mode - Trade Complete |
| 205 | Unknown Fanfare A |
| 206 | Unknown Fanfare B |
| 207 | Unknown SFX A |
| 208 | Unknown SFX B |
| 209 | Unused Phantom Hourglass Boss Theme |
| 210 | Unused Phantom Hourglass Theme |
| 211 | Unused Song A |
| 212 | Unused Song B |
