What You Believe Might Not Be: The Best of Prototype
| Track | Durée | Titre | Tablature |
| 1 | 05:22 | The Way It Ends | oui |
| 2 | 05:02 | Trinity | |
| 3 | 04:43 | Seed | |
| 4 | 07:06 | Cynic Dreams | |
| 5 | 04:31 | Live a Lie | oui |
| 6 | 04:52 | Catalyst | |
| 7 | 05:07 | Shine (demo) | |
| 8 | 04:22 | Heart Machine | |
| 9 | 04:19 | Chrysalis | |
| 10 | 04:53 | Pure | |
| 11 | 06:15 | The Chosen Ones | |
| 12 | 06:56 | Dead of Jericho (demo) | |
| 13 | 08:12 | My Own Deception | |
| 14 | 03:24 | Synthespian |