| 1 | Trinity in a Jam | 00:00:00 |
| 2 | Impossible Pursuit | 00:03:26.1340000 |
| 3 | Follow Instructions | 00:06:35.8350000 |
| 4 | The Question | 00:09:42.6350000 |
| 5 | "They're Coming for You" | 00:11:58.1350000 |
| 6 | Unable to Speak | 00:16:47.0030000 |
| 7 | Getting the Bug Out | 00:21:31.8050000 |
| 8 | Morpheus' Proposal | 00:25:07.6740000 |
| 9 | Down the Rabbit Hole | 00:28:49.9740000 |
| 10 | Slimy Rebirth | 00:32:23.8420000 |
| 11 | Nebuchadnezzar's Crew | 00:35:20.1760000 |
| 12 | The Real World | 00:38:39.0100000 |
| 13 | The Search Is Over | 00:44:20.5110000 |
| 14 | Training Begins | 00:46:31.1780000 |
| 15 | Morpheus/Neo Matchup | 00:48:55.4780000 |
| 16 | First Jump | 00:53:28.6460000 |
| 17 | The Gatekeepers | 00:56:29.1460000 |
| 18 | Running Silent and Deep | 00:58:58.1460000 |
| 19 | Dealing for Bliss | 01:01:05.3470000 |
| 20 | Off to See the Oracle | 01:05:13.1480000 |
| 21 | There Is No Spoon | 01:07:43.1820000 |
| 22 | Choices...and a Cookie | 01:12:29.6830000 |
| 23 | Glitch in the Matrix | 01:17:45.4840000 |
| 24 | One Left Behide | 01:20:58.8190000 |
| 25 | Heroes Unplugged | 01:25:00.8190000 |
| 26 | Cypher's Burnout | 01:29:40.1550000 |
| 27 | Matters of Belief | 01:31:22.6550000 |
| 28 | Virus to Be Cured | 01:37:19.9910000 |
| 29 | Lobby Shooting Spree | 01:40:59.3250000 |
| 30 | Dodge This | 01:44:14.6930000 |
| 31 | Gotcha | 01:46:54.6630000 |
| 32 | Rooftop Rescue | 01:50:12.3300000 |
| 33 | Subway Showdown | 01:52:50.3310000 |
| 34 | "My Name Is Neo" | 01:56:30.4980000 |
| 35 | Sentinels Attack | 01:58:42.8650000 |
| 36 | "He Is the One" | 02:02:20.6670000 |
| 37 | Final Connections | 02:05:34.8360000 |
| 38 | End Credits ("Wake Up Rock Is Dead") | 02:08:39.6700000 |