| Disc 1 |
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| 01 Main Title (2:01) |
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| PART I |
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| 02 Erasmus (2:11) |
| 03 Reef (2:04) |
| 04 Wakening in the Japans (2:20) |
| 05 In the Village (1:14) |
| 06 Yabu's Arrival (1:22) |
| 07 One of You Is to Die (0:51) |
| 08 I'm Not the One to Go (2:47) |
| 09 Boiling Torture (0:52) |
| 10 A Slave Ship (1:18) |
| 11 Do It, Ingles (1:13) |
| 12 Men Make Mistakes (2:17) |
| 13 After the Rescue (0:46) |
| 14 I Got Drunk Last Night (0:39) |
| 15 Naga (1:21) |
| 16 On the Way to Meet Toranaga (4:47) |
| 17 Sent to Prison (2:35) |
| 18 In the Cellblock (3:41) |
| 19 Anjin-San (1:46) |
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| PART II |
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| 20 Put Them On (2:45) |
| 21 Blackthorne and Mariko (0:56) |
| 22 Alvito (0:59) |
| 23 Something Unexpected (0:35) |
| 24 Amida Tong (3:18) |
| 25 Kasiji Yabuka (1:00) |
| 26 You Will Burn in Hell* (2:31) |
| 27 A Big-Hatted Person (1:41) |
| 28 Ishido's Letter* (3:34) |
| 29 A Honeyed Tongue (1:46) |
| 30 The Ambush (5:21) |
| 31 To the Galley! (4:42) |
| 32 An Easy Target (1:46) |
| 33 Come Aboard (2:10) |
| 34 A Nice Deal (3:50) |
| 35 Coming Back to Anjiro (1:24) |
| 36 Only Japanese Ways (0:41) |
| 37 End Credits (alternate) (0:53) |
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| Disc 2 |
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| 01 Mariko's Theme (3:04) |
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| PART III |
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| 02 Challenging Omi (2:47) |
| 03 Seppuku (2:57) |
| 04 Tonight (1:24) |
| 05 Training (0:58) |
| 06 Nocturne (2:08) |
| 07 Confrontation (2:37) |
| 08 Wife Beating (2:39) |
| 09 Please Don't Do This (2:13) |
| 10 Punishment (0:56) |
| 11 Elegy (1:04) |
| 12 Earthquake (2:18) |
| 13 A Casualty (1:09) |
| 14 Toranaga's Camp (1:44) |
| 15 Samurai (3:07) |
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| PART IV |
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| 16 Kiku (1:20) |
| 17 To Yedo (4:25) |
| 18 Before the Ceremony (0:34) |
| 19 Tea Ceremony (5:29) |
| 20 Swear to Me (3:25) |
| 21 Unhappy Lovers (0:46) |
| 22 Learning Japanese (1:32) |
| 23 Kinjiru (1:30) |
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| PART V |
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| 24 Blackthorne and Fujiko (1:36) |
| 25 Samurai's Oath (1:13) |
| 26 Erasmus Towed (1:52) |
| 27 Preparing for Mariko's Suicide (2:19) |
| 28 Yabu Trapped (1:10) |
| 29 Yabu's Betrayal (1:07) |
| 30 Yabu and Ninja (2:07) |
| 31 Mariko's Funeral (1:13) |
| 32 Christian Samurai (1:47) |
| 33 Vinck's Madness (3:06) |
| 34 Mariko (unused) (3:04) |
| 35 Finale (3:53) |
| 36 End Credits (0:53) |
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| Disc 3 |
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| THE ALBUM |
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| 01 Shōgun (2:38) |
| 02 The Japans (2:23) |
| 03 Tea and Jealousy (5:29) |
| 04 Nocturne (2:07) |
| 05 Toranaga (2:15) |
| 06 To the Galley! (3:08) |
| 07 Mariko (3:04) |
| 08 Ceremonial (2:11) |
| 09 Despair and Madness (3:06) |
| 10 Anjiro (2:16) |
| 11 Blackthorne (2:57) |
| 12 Escape From Osaka* (3:34) |
| 13 Finale (2:38) |
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| THE EXTRAS |
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| 14 Bumpers (0:26) |
| 15 Wakening in the Japans (original version) (2:12) |
| 16 Decapitation (0:49) |
| 17 Blackthorne Taken in the Pit (0:28) |
| 18 The Shortest Straw (1:26) |
| 19 Pieterzoon's Death (0:40) |
| 20 After the Night of Screams (0:37) |
| 21 Cleaning Humiliation (1:18) |
| 22 A Good Bath (0:46) |
| 23 Kiku-San (2:50) |
| 24 Do It, Ingles (original version) (1:12) |
| 25 Do It, Ingles (pickup A) (0:09) |
| 26 Do It, Ingles (pickup B) (0:09) |
| 27 Blackthorne at the Wheel (original version) (0:56) |
| 28 So I Owe You My Life, Ingles (0:35) |
| 29 I Got Drunk Last Night (original version) (0:46) |
| 30 Blackthorne Obeys Naga (0:26) |
| 31 Sake to Me (2:46) |
| 32 Stripped (0:16) |
| 33 Put Them On (pickup) (0:14) |
| 34 Moon Over Osaka (3:30) |
| 35 Melancholy Shamisen and Shakuhachi (2:53) |
| 36 Shamisen Source (2:16) |
| 37 Tono (0:42) |
| 38 Blackthorne's Dance (unused)* (0:46) |
| 39 You Will Burn in Hell (alternate A) (0:15) |
| 40 You Will Burn in Hell (alternate B) (0:13) |
| 41 Night March (0:18) |
| 42 To the Galley! (original version) (3:09) |
| 43 Any Closer, And… (0:26) |
| 44 Now! (0:57) |
| 45 Elegy (alternate) (1:06) |
| 46 To Yedo II (short version) (1:19) |
| 47 An Empty Cup (1:36) |
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| *Contains "Blackthorne's Shanty" by Eric Bercovici |
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