| 1 | Opening |
| 2 | Chapter 1: The Return of Palutena |
| 3 | Chapter 1: That First Town |
| 4 | Boss Battle 1 |
| 5 | Chapter 2: Magnus and the Dark Lord |
| 6 | Chapter 2: Dark Lord Gaol's Castle |
| 7 | Magnus's Theme |
| 8 | Chapter 3: Heads of the Hewdraw |
| 9 | Chapter 3: That Burning Town |
| 10 | Chapter 4: The Reaper's Line of Sight |
| 11 | Chapter 4: Reaper Fortress |
| 12 | Chapter 5: Pandora's Labyrinth of Deceit |
| 13 | Chapter 5: Into the Labyrinth |
| 14 | Chapter 6: Dark Pit |
| 15 | Chapter 6: Ruins of the Temple |
| 16 | Dark Pit's Theme |
| 17 | Chapter 7: The Seafloor Palace |
| 18 | Chapter 7: At the Seafloor Palace |
| 19 | Chapter 8: The Space-Pirate Ship (Route A) |
| 20 | Chapter 8: The Space-Pirate Ship (Route B) |
| 21 | Chapter 8: In the Space-Pirate Ship |
| 22 | Chapter 9: Medusa's Final Battle |
| 23 | Chapter 9: Underworld Gatekeeper |
| 24 | Chapter 9: Underworld Castle Entrance |
| 25 | Chapter 9: Underworld Castle |
| 26 | Boss Battle 2 |
| 27 | False Ending |
