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Disc1
| 1 | Prologue | Bruce Broughton | 0:58 |
| 2 | Main Title / Major Mayhem | Bruce Broughton | 4:07 |
| 3 | Hologram Gags / You’ll Do (alternate) | Bruce Broughton | 1:05 |
| 4 | Meet Dr. Smith | Bruce Broughton | 1:40 |
| 5 | Dog Tags, No. 1 | Bruce Broughton | 0:38 |
| 6 | Reprogram the Robot / The Launch | Bruce Broughton | 6:25 |
| 7 | Bad Dream / The Robot Attack | Bruce Broughton | 3:22 |
| 8 | Where’s Judy? / Judy Is Dying (remix) | Bruce Broughton | 6:23 |
| 9 | Can’t Kill the Man (revised) | Bruce Broughton | 0:49 |
| 10 | We’re Lost | Bruce Broughton | 0:23 |
| 11 | The Proteus (alternate) | Bruce Broughton | 2:23 |
| 12 | Boarding the Proteus, Pt. 1 / Boardingthe Proteus, Pt. 2 | Bruce Broughton | 7:01 |
| 13 | Spiders and Static / Spiders Attack (revised) | Bruce Broughton | 7:54 |
| 14 | Jupiter Crash | Bruce Broughton | 1:11 |
| 15 | A Strange New Place / Spider Scratch | Bruce Broughton | 1:29 |
| 16 | Matt and Judy | Bruce Broughton | 1:40 |
| 17 | Goodnights | Bruce Broughton | 0:38 |
| 18 | Energy Bubbles / Dog Tags, No. 2 / John and West Set Out | Bruce Broughton | 2:23 |
| 19 | Will’s Walk / Smith Persuades Will | Bruce Broughton | 1:56 |
| 20 | Will and Smith Set Out | Bruce Broughton | 1:59 |
| 21 | Decades Old / I’m Your Son (revised) / Time Machine | Bruce Broughton | 4:27 |
Disc2
| 1 | Never Trust Anyone / Smith Interrupts / Spider Smith | Bruce Broughton | 3:01 |
| 2 | Friendship / We Have a Plan / Kill the Monster (revised) | Bruce Broughton | 8:46 |
| 3 | Let’s Go Major (original) | Bruce Broughton | 1:26 |
| 4 | The Portal (revised alternate) | Bruce Broughton | 2:44 |
| 5 | Through the Planet (revised alternate) | Bruce Broughton | 2:28 |
| 6 | Nice Work Fly Boy (revised) | Bruce Broughton | 1:36 |
| 7 | Fanfare for Will | Bruce Broughton | 0:27 |
| 8 | Lost in Space | Bruce Broughton | 3:26 |
| 9 | Hologram Gags / You’ll Do (original) | Bruce Broughton | 1:04 |
| 10 | Can’t Kill the Man (original) | Bruce Broughton | 0:49 |
| 11 | The Proteus (original) | Bruce Broughton | 2:24 |
| 12 | Spiders and Static / Spiders Attack (original) | Bruce Broughton | 7:54 |
| 13 | Decades Old / I’m Your Son (original) / Time Machine | Bruce Broughton | 4:32 |
| 14 | Friendship / We Have a Plan / Kill the Monster (original) | Bruce Broughton | 8:50 |
| 15 | Let’s Go Major (alternate) | Bruce Broughton | 1:24 |
| 16 | The Portal (original) | Bruce Broughton | 2:42 |
| 17 | The Portal (revised) | Bruce Broughton | 2:43 |
| 18 | Through the Planet (original) | Bruce Broughton | 3:13 |
| 19 | Through the Planet (revised) | Bruce Broughton | 2:41 |
| 20 | Nice Work Fly Boy (original) | Bruce Broughton | 1:48 |