| 1 | The Pokémon Company Logo | Tsukasa Tawada | 0:03 |
| 2 | Genius Sonority Logo | Tsukasa Tawada | 0:07 |
| 3 | Title Screen | Tsukasa Tawada | 1:41 |
| 4 | Game Demo | Tsukasa Tawada | 1:31 |
| 5 | Game Demo (SFX) | Tsukasa Tawada | 1:31 |
| 6 | Main Menu - Lobby - Bonus Disc Menu | Tsukasa Tawada | 2:47 |
| 7 | Wes Steals the Snatching Machine | Tsukasa Tawada | 1:03 |
| 8 | Wes Steals the Snatching Machine (SFX) | Tsukasa Tawada | 1:05 |
| 9 | Wind (SFX) | Tsukasa Tawada | 1:06 |
| 10 | Outskirt Stand | Tsukasa Tawada | 0:59 |
| 11 | News 1 | Tsukasa Tawada | 0:33 |
| 12 | Normal Battle | Tsukasa Tawada | 2:02 |
| 13 | Win Battle | Tsukasa Tawada | 0:05 |
| 14 | World Map | Tsukasa Tawada | 1:14 |
| 15 | Team Snagem Battle - Colosseum Round 1 Battle | Tsukasa Tawada | 1:55 |
| 16 | Level Up | Tsukasa Tawada | 0:02 |
| 17 | Rui Joins Wes | Tsukasa Tawada | 0:03 |
| 18 | Phenac City | Tsukasa Tawada | 4:15 |
| 19 | Pokémon Center | Tsukasa Tawada | 1:26 |
| 20 | Heal Pokémon | Tsukasa Tawada | 0:03 |
| 21 | Trainers' School | Tsukasa Tawada | 1:09 |
| 22 | Get Item | Tsukasa Tawada | 0:03 |
| 23 | Es Cade's Theme | Tsukasa Tawada | 1:13 |
| 24 | Snagem Hideout | Tsukasa Tawada | 1:21 |
| 25 | Cipher Syndicate's Theme | Tsukasa Tawada | 1:04 |
| 26 | Miror B.'s Retro Groove | Tsukasa Tawada | 1:53 |
| 27 | Snatch Shadow Pokémon | Tsukasa Tawada | 0:05 |
| 28 | Cipher Peon Battle - Colosseum Round 2 Battle | Tsukasa Tawada | 2:41 |
| 29 | Pyrite Town | Tsukasa Tawada | 3:48 |
| 30 | Pyrite Building | Tsukasa Tawada | 1:49 |
| 31 | Colosseum Battle Round 1 Intro | Tsukasa Tawada | 0:13 |
| 32 | Colosseum Battle Round 2 Intro | Tsukasa Tawada | 0:13 |
| 33 | Colosseum Battle Round 3 Intro | Tsukasa Tawada | 0:13 |
| 34 | Colosseum Round 3 Battle | Tsukasa Tawada | 3:07 |
| 35 | Colosseum Battle Round 4 Intro | Tsukasa Tawada | 0:13 |
| 36 | Colosseum Round 4 Battle - Cipher Admin Battle | Tsukasa Tawada | 2:18 |
| 37 | Mirakle B.'s Imitation Groove | Tsukasa Tawada | 1:34 |
| 38 | Fadeen the Fortuneteller | Tsukasa Tawada | 2:09 |
| 39 | Evolution Jingle | Tsukasa Tawada | 0:03 |
| 40 | Pokémon is Evolving | Tsukasa Tawada | 1:00 |
| 41 | Congratulations | Tsukasa Tawada | 0:04 |
| 42 | Agate Village | Tsukasa Tawada | 2:26 |
| 43 | Relic Forest in Danger | Tsukasa Tawada | 0:43 |
| 44 | Relic Forest | Tsukasa Tawada | 1:55 |
| 45 | Time Flute | Tsukasa Tawada | 0:05 |
| 46 | Shadow Pokémon is Purified | Tsukasa Tawada | 0:09 |
| 47 | Mt. Battle Rest Room | Tsukasa Tawada | 1:26 |
| 48 | Mt. Battle | Tsukasa Tawada | 1:09 |
| 49 | Shadow Pokémon Lab | Tsukasa Tawada | 1:33 |
| 50 | Shadow Pokémon Lab Alarm | Tsukasa Tawada | 0:15 |
| 51 | The Under | Tsukasa Tawada | 2:10 |
| 52 | News 2 | Tsukasa Tawada | 0:35 |
| 53 | Realgam Tower | Tsukasa Tawada | 1:52 |
| 54 | Nascour's Theme | Tsukasa Tawada | 1:05 |
| 55 | Nascour's Theme (SFX) | Tsukasa Tawada | 1:05 |
| 56 | Evice Theme | Tsukasa Tawada | 1:07 |
| 57 | Final Battle | Tsukasa Tawada | 2:25 |
| 58 | Ending A | Tsukasa Tawada | 1:38 |
| 59 | Ending B | Tsukasa Tawada | 0:11 |
| 60 | Ending B (SFX) | Tsukasa Tawada | 0:11 |
| 61 | Staff Roll (JP) | Tsukasa Tawada | 2:44 |
| 62 | Staff Roll (US-EU) | Tsukasa Tawada | 2:52 |
| 63 | News 3 | Tsukasa Tawada | 0:31 |
| 64 | Battle Mode Menu | Tsukasa Tawada | 3:36 |
| 65 | Vs. Mode Battle #1 | Tsukasa Tawada | 2:20 |
| 66 | Vs. Mode Battle #2 | Tsukasa Tawada | 2:13 |
| 67 | Vs. Mode Battle #3 | Tsukasa Tawada | 3:06 |
| 68 | Get PDA Mail 1 | Tsukasa Tawada | 0:03 |
| 69 | Get PDA Mail 2 | Tsukasa Tawada | 0:03 |
| 70 | Get PDA Mail 3 | Tsukasa Tawada | 0:02 |
| 71 | Get PDA Mail 4 | Tsukasa Tawada | 0:01 |
| 72 | Get PDA Mail 5 | Tsukasa Tawada | 0:01 |
| 73 | Get PDA Mail 6 | Tsukasa Tawada | 0:02 |
| 74 | Get PDA Mail 7 | Tsukasa Tawada | 0:03 |
| 75 | Get PDA Mail 8 | Tsukasa Tawada | 0:02 |
| 76 | Get PDA Mail 9 | Tsukasa Tawada | 0:02 |
| 77 | Get PDA Mail 10 | Tsukasa Tawada | 0:02 |
| 78 | JP Bonus Disc - Donkey Kong Country GBC Trailer | Tsukasa Tawada | 0:21 |
| 79 | JP Bonus Disc - Donkey Konga Trailer | Tsukasa Tawada | 1:17 |
| 80 | JP Bonus Disc - F-Zero GP Legend Trailer | Tsukasa Tawada | 0:23 |
| 81 | JP Bonus Disc - Mario & Luigi Superstar Saga Trailer | Tsukasa Tawada | 0:51 |
| 82 | JP Bonus Disc - Mario Kart Double Dash! Trailer | Tsukasa Tawada | 1:01 |
| 83 | JP Bonus Disc - Mario Party 5 Trailer | Tsukasa Tawada | 0:48 |
| 84 | JP Bonus Disc - Pokémon Box Ruby & Sapphire Trailer | Tsukasa Tawada | 2:21 |
| 85 | US Bonus Disc - Pokémon Colosseum Trailer | Tsukasa Tawada | 3:15 |
| 86 | US Bonus Disc - Jirachi the Wish Maker | Tsukasa Tawada | 1:35 |
| 87 | US Bonus Disc - Pokémon Center Theme | Tsukasa Tawada | 1:28 |
| 88 | US Bonus Disc - Receiving Jirachi | Tsukasa Tawada | 0:32 |
| 89 | US Bonus Disc - Fanfare 1 | Tsukasa Tawada | 0:04 |
| 90 | US Bonus Disc - Fanfare 2 | Tsukasa Tawada | 0:02 |
| 91 | US Bonus Disc - Fanfare 3 | Tsukasa Tawada | 0:05 |
| 92 | US Bonus Disc - Fanfare 4 | Tsukasa Tawada | 0:04 |
| 93 | US Bonus Disc - Fanfare 5 | Tsukasa Tawada | 0:03 |
| 94 | ex tre (Unused) | Tsukasa Tawada | 0:03 |
| 95 | Virtual (Unused) | Tsukasa Tawada | 0:58 |
| 96 | winwin (Unused) | Tsukasa Tawada | 0:02 |
| 97 | US Bonus Disc Menu Music (Unused) | Tsukasa Tawada | 1:47 |