| Disc 1 |
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| 01 Main Title* (2nd Season, Soprano Version, Enhanced Stereo) 1:01 |
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| WHO MOURNS FOR ADONAIS? (Total Time: 29:07) |
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| 02 Ship of Stars/Green Hand M11/M12 1:51 |
| 03 Giant Hand M13 1:13 |
| 04 Apollo Motif M14/M14A 1:12 |
| 05 Apollo's Power/Kirk's Theme/Apollo's Temple M21/M22/M23 3:16 |
| 06 Stingers/Giant Apollo M24/M24A/M24B/M24C/M24D/M25 1:03 |
| 07 Spaceship Stuck/Apollo Fades/Kirk to Apollo M26/M27/M28 1:17 |
| 08 Apollo Digs Carolyn/Apollo's Fist/New Venus M29–30/M31/M32 2:38 |
| 09 Computer Generator M33 0:34 |
| 10 Apollo's Temple #2 M34 2:58 |
| 11 Apollo Zaps M35–40 1:02 |
| 12 Apollo Weakens/Kirk to Enterprise/Bridge to Apollo M41/M42/M43 1:14 |
| 13 Kirk Worried M44–50 0:41 |
| 14 Apollo in Love M51 0:44 |
| 15 Dreamy Venus/Kirk and Carolyn/Spaceship Stuck Again M52/M53/M54 2:34 |
| 16 Apollo's Kiss/Apollo's Storm/Final Battle M55/M56-60/M61 3:35 |
| 17 End of Apollo/Spaceship Orbit† M62/M63 2:48 |
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| MIRROR, MIRROR (Total Time: 13:59) |
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| 18 Mirror Mirror/Blackship Theme/The Agonizer M12/M12A/M12B 2:23 |
| 19 Blackship in Space/Blackship Underscore M13/M14 1:21 |
| 20 Thematic Bridge*/Blackship Tension M21/M21A 2:19 |
| 21 Suspicion M23 1:13 |
| 22 Evil Kirk/Evil Kirk #2 M32/M33 0:38 |
| 23 Meet Marlena/Short Curtain M36/37 2:01 |
| 24 Blackship Theme M12AA 0:47 |
| 25 Pretty Marlena M46 1:21 |
| 26 Goodbye Marlena M47–50 1:41 |
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| BY ANY OTHER NAME (Total Time: 12:28) |
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| 27 Kelvan Theme/Neutralizer M12/M12A+M12AS 1:31 |
| 28 More Neutralizer M14 0:55 |
| 29 Rojan's Revenge/Rojan's Blocks/Broken Block M22/M23/M24 3:04 |
| 30 More Blocks/Rallentando M41/M42 2:05 |
| 31 Pretty Words/Short Playoff M52/M55 1:48 |
| 32 Kelinda's Question/Rojan Roars/Kelinda's Kiss M59/M61/M61A 1:40 |
| 33 Finale/Thematic Playoff*† M64/M64A 1:13 |
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| THE OMEGA GLORY (Total Time: 2:02) |
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| 34 Drums 0:20 |
| 35 Star-Spangled Enterprise (act out)* MX-1/MX-6 0:21 |
| 36 Star-Spangled Enterprise (episode medley)* MX-5/MX-4/MX-2 0:38 |
| 37 Star-Spangled Enterprise (outtakes medley)* MX-3/MX-7/MX-6 0:37 |
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| SECOND SEASON LIBRARY MUSIC (Total Time: 14:25) |
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| From "Who Mourns for Adonais?" |
| 38 Kirk to Apollo M28A 0:26 |
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| From "Mirror, Mirror" |
| 39 The Agonizer M12BA 0:26 |
| 40 Blackship in Space M13A 0:39 |
| 41 Blackship in Space M13B 0:22 |
| 42 Blackship Tension M21AA 1:03 |
| 43 Blackship Tension M21A 0:36 |
| 44 Suspicion M23A 0:38 |
| 45 Meet Marlena M36A 0:49 |
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| From "By Any Other Name" |
| 46 Kelvan Theme M12 tk 5 0:40 |
| 47 Neutralizer M12AA 1:00 |
| 48 Rojan's Blocks M23A tk 3 0:41 |
| 49 Short Playoff M55A 0:15 |
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| From "Charlie X" |
| 50 Chess Game (M32, recorded with "Who Mourns for Adonais?") LM50 1:25 |
| 51 Zap Sam (M41, recorded with "Who Mourns for Adonais?") LM51 1:11 |
| 52 Goodbye Charlie (M62, 2 versions, recorded with "By Any Other Name") LM53 1:32 |
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| From "The Corbomite Maneuver" |
| 53 Fesarius Approaches (M31A, recorded with "Mirror, Mirror") LM52 2:16 |
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| 54 End Title* (2nd Season, Soprano Version, Enhanced Stereo) 0:47 |
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| Disc 2 |
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| ELAAN OF TROYIUS (Total Time: 31:08) |
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| 01 Mission to Elas/Meet Kryton/Meet Elaan M11/M12/M13 2:24 |
| 02 Elaan of Elas/Impulse Drive/Elaan Is Annoyed/Peevish Elaan/Thematic |
| Bridge*/Elaan's Interest M15/M16/M17/M21/M22/M23 2:40 |
| 03 Mysterious Things/Klingon Warship/Elaan in Trouble M24/M25/M26 2:01 |
| 04 Medical Man/Elaan Motif/Elaan Eats M27/M28/M29–30 1:00 |
| 05 Elaan Angry/Enemy Warship/Bad Kryton M31/M32/M33 2:57 |
| 06 More Trouble/Elaan's Temper M34/M35 1:23 |
| 07 Magic Tears/The Intruder/Kryton Vanishes M36–40/M41/M42 3:40 |
| 08 Afterwards M43 1:26 |
| 09 Realization/Battle Stations M44/M45 1:54 |
| 10 Close Call M46 1:12 |
| 11 Elaan Pleads M51 1:34 |
| 12 Klingon Command M52 1:56 |
| 13 Elaan's Jewels/Confrontation M53/M54 1:55 |
| 14 Battle Music M55–60 2:06 |
| 15 Thematic Bridge*/Goodbye Elaan/Kirk in Command M61/M62/M63 2:28 |
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| SPOCK'S BRAIN (Total Time: 33:00) |
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| 16 Alien Ship/Meet Kara M11/M12 3:09 |
| 17 Awakening/Poor Spock M13/M14 1:26 |
| 18 No Mind/Tense Moment/Tracking the Alien/The Question M15/M16/M21/M22A/M22 2:31 |
| 19 Icy Planet/Caveman/Caveman Fight M23/M24/25 2:56 |
| 20 Caveman Run/Cave Music/Corpus Spock/Hello Luma/Kara Zaps Kirk M31/M32/M33/M34/M36 4:06 |
| 21 Chicken Delight/Kirk Caught/The Answer/The Agonizer/Sulu's Log M41/M42/M43/M44/M45 2:57 |
| 22 Communicators/Scientific Fight M46/M47A 1:54 |
| 23 Spock Walks/Agonizer #2/Spooky Spock M49–50+M50A/M51/M52 tk 3 3:54 |
| 24 Magic Helmet/Kara's Kaper M53/M54 1:50 |
| 25 Kara Commands M55 0:52 |
| 26 Kirk's Dilemma/Magic Helmet #2/Operation Spock/Operation Montage/Spock Is O.K./Spock's Fugue M56/M57–60/M61/M62/M63/M64 7:05 |
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| THIRD SEASON LIBRARY MUSIC (Total Time: 12:52) |
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| From "Elaan of Troyius" |
| 27 Meet Elaan M13A 0:33 |
| 28 Elaan in Trouble M26A 0:14 |
| 29 Bad Kryton M33A/M33B 1:24 |
| 30 Battle Stations M45A 1:01 |
| 31 Goodbye Elaan M62A 0:16 |
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| From "Spock's Brain" |
| 32 Meet Kara M12A 0:29 |
| 33 Poor Spock M14A/M14B 0:21 |
| 34 The Question M22A 0:38 |
| 35 Kara Motif M26 0:10 |
| 36 Corpus Spock M33A 0:33 |
| 37 Hello Luma M34A/M34B 1:29 |
| 38 Scientific Fight M47 0:32 |
| 39 Overstings M48A 0:30 |
| 40 Spooky Spock With Overstings M52 tk 3+M48A 1:14 |
| 41 Brain Box M50A 0:09 |
| 42 Spooky Spock M52 tk 4 1:11 |
| 43 Kara's Kaper M54A 0:29 |
| 44 Kara Motif (Fred Steiner rehearsal and master) M26 0:57 |
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| * Contains "Theme From STAR TREK (TV Series)" by Alexander Courage and Gene Roddenberry |
| † Based on a theme by Alexander Courage |
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