| 1 | Intro Story |
| 2 | Main Theme (Title Screen) |
| 3 | Peach and the Mysterious Map |
| 4 | Mail for the Mario Bros. |
| 5 | Adventure Begins |
| 6 | All Aboard to Rogueport |
| 7 | Chapter Introduction |
| 8 | Rogueport |
| 9 | X-Nauts Attack |
| 10 | Event Battle |
| 11 | Victory without Partner |
| 12 | Level Up! |
| 13 | New Party Member |
| 14 | Learning a New Skill |
| 15 | Game Over |
| 16 | Goodnight Mario |
| 17 | Professor Frankly |
| 18 | Badge Get |
| 19 | Tutorial Battle |
| 20 | Rogueport Sewers |
| 21 | Battle Theme |
| 22 | Battle Won! |
| 23 | Item Get |
| 24 | Special Item Get |
| 25 | Curse of the Black Box |
| 26 | Ruins of the Thousand-Year Door |
| 27 | Petal Meadows |
| 28 | Star Piece Get |
| 29 | Hooktail Flies Over |
| 30 | Puzzle Solved! |
| 31 | Petalburg |
| 32 | You've Got Mail! |
| 33 | Super Fun Quirk Quiz |
| 34 | Question (Super Fun Quirk Quiz) |
| 35 | Shhwonk Fortress |
| 36 | Entering Hooktail's Castle |
| 37 | Hooktail's Castle |
| 38 | Escape the Falling Ceiling |
| 39 | Ms. Mowz's Theme |
| 40 | Hooktail's Theme |
| 41 | Hooktail Battle |
| 42 | Reunion |
| 43 | Crystal Star Get |
| 44 | End of Chapter |
| 45 | Grodus' Room |
| 46 | Peach's Theme |
| 47 | Bowser's Castle |
| 48 | Peach's E-Mail |
| 49 | Power-Up Partner |
| 50 | Luigi's Theme |
| 51 | The Punies |
| 52 | Boggly Woods |
| 53 | Shadow Sirens |
| 54 | The Great Boggly Tree |
| 55 | Missing Fanfare |
| 56 | Shadow Sirens Battle |
| 57 | Madame Flurrie |
| 58 | Jabbies Battle |
| 59 | Lord Crump's Theme |
| 60 | Magnus von Grapple's Theme |
| 61 | Magnus von Grapple Battle |
| 62 | TEC's Walts |
| 63 | Bowser's Theme |
| 64 | Super Koopa Bros. World 1 |
| 65 | Super Koopa Bros. World 1 (Hurry Up!) |
| 66 | Super Koopa Bros. (Invincibility) |
| 67 | Super Koopa Bros. (World Clear) |
| 68 | Super Koopa Bros. (Lose Life) |
| 69 | Cooking with Zess T. |
| 70 | Ishnail Theme |
| 71 | Pianta Parlor |
| 72 | Pianta Parlor Mini-Game |
| 73 | Cheep-Cheep Blimp |
| 74 | Glitzville |
| 75 | Glitz Pit |
| 76 | Grubba's Theme |
| 77 | Glitz Pit Intro |
| 78 | Glitz Pit Lose |
| 79 | Glitz Pit Outro |
| 80 | Bouncing Yoshi Egg |
| 81 | Mystery E-Mail |
| 82 | Glitz Pit Mysteries |
| 83 | Rawk Hawk Battle |
| 84 | Rawk Hawk Defeated |
| 85 | Macho Grubba's Theme |
| 86 | Macho Grubba Battle |
| 87 | Sadness and Happiness |
| 88 | Twilight Trail |
| 89 | Twilight Town |
| 90 | Creepy Steeple |
| 91 | Doopliss Theme |
| 92 | Doopliss Battle |
| 93 | Super Koopa Bros. World 2 |
| 94 | Super Koopa Bros. World 2 (Hurry Up!) |
| 95 | Whoa! |
| 96 | Ghostly Encounter |
| 97 | Ship Under Attack! |
| 98 | Keelhaul Key |
| 99 | Pirate's Grotto |
| 100 | Cortez's Theme |
| 101 | Cortez Battle |
| 102 | Enemy Revealed |
| 103 | Grodus' Computer |
| 104 | The Black Skull |
| 105 | Train Travel |
| 106 | Excess Express at Day |
| 107 | Detective Pennington |
| 108 | Ooh Fanfare |
| 109 | Wrong |
| 110 | Excess Express at Dusk |
| 111 | Excess Express at Night |
| 112 | Riverside Station |
| 113 | Smorgs Battle |
| 114 | Poshley Heights |
| 115 | Poshley Sanctum |
| 116 | Grodus' Theme |
| 117 | Super Koopa Bros. World 3 |
| 118 | Super Koopa Bros. World 3 (Hurry Up!) |
| 119 | Fahr Outpost |
| 120 | Blast-off to the Moon |
| 121 | The Moon |
| 122 | X-Naut Fortress |
| 123 | 8-bit Mario |
| 124 | Palace of Shadow |
| 125 | Riddle Tower |
| 126 | Deeper into the Shadows |
| 127 | Grodus Battle |
| 128 | Bowser Battle |
| 129 | Shadow Queen's Awakening |
| 130 | Shadow Queen's Theme |
| 131 | Shadow Peach Battle |
| 132 | Invincible Shadow Queen Battle |
| 133 | We're Counting on You, Mario! |
| 134 | Final Battle |
| 135 | Peach is Saved |
| 136 | Return to Mushroom Kingdom |
| 137 | Farewell Rogueport |
| 138 | Last Look at Rogueport |
| 139 | Here We Go Again |
| 140 | Credits |
| 141 | Pit of 100 Trials |
| 142 | Riverside Station (Beta) |
| 143 | Debug Menu (Unused) |
| 144 | Main Theme (No Intro) |
| 145 | Main Theme (Japanese) |
| 146 | Super Koopa Bros. World 1 (Hurry Up! (No Intro)) |
| 147 | Mail for the Mario Bros. (No Intro) |
