Intros 0:00
Beginning 3:10
Undercaves 6:52
The Vents 9:03
The Lagoon 14:00
Ridge Water 20:20
Open Ocean 23:35
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Ice Zone 24:39
Hard Water 25:48
Cold Water (The Big Blue) 27:12
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Open Ocean Return (Not on Cartridge) 30:37
Island Zone 31:41
Deep Water (The Asterite) 33:34
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(The following 5 stages are not on the Cartridge version)
Volcanic Reef 36:21
Ship Grave Sea 38:06
Wreck Trap 40:16
The Sea of Silence 42:22
Deep Gate 44:27
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The Marble Sea 49:22
The Library 51:02 (A few FMV clips)
Deep City 1:00:52
City of Forever (shortcut) 1:02:59
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Jurassic Beach 1:04:14
Pteranodon Pond 1:06:14
Origin Beach 1:09:05
Trilobite Circle 1:10:56
Dark Water (The Asterite Boss) 1:11:58
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Deep Water (Return to The Asterite) 1:13:19
City of Forever (Full Route) 1:15:18
Back in Time 1:18:27
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The Tube 1:19:15
The Machine 1:21:12
Vortex Queen 1:27:18

Final Boss Defeated & Ending 1:29:09
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Played the Japanese version to see if there's any real difference between this and the US version - none except the text. The subtitles are copied verbatim from the text of the US version and, as I can't read Japanese, I don't know if they are accurate to what the Japanese text actually says.