After reading this case for many many times, I believe it's missing some critical information that can help solve the case.
All I was able to make up from reading this, is that Parker Poderi and Jeremy Daniels are the same 2 men that were sitting on the outer deck of Bella Fortuna 21 years ago, and that Parker Poderi is the one who went to the captain before leaving the ship, and left a paper with the letters "P.D" on it in his pocket. I also think that after leaving Bella Fortuna on that stormy night, both Parker and Jeremy weren't able to remember the exact location of the ship, and hence they decided to join the US coastguard to help them find it.
About what the 2 guys at the bottom deck were able to hear, I believe it's some kind of recording that was recorded few seconds before the death of all the passengers on Bella Fortuna 21 years ago, and that the green thing in the air that the girl was referring to was the toxic gas that was released in the ship at that time.