This song is about someone getting abducted, and at first is scared to death! But once he is released, he realizes how much better it would have been to just stay on the mothership(My soul felt so safe up there; no self-centered natives destroying our earth). He is called insane, and possibly commited?
Before the aliens returned him they just left him with one bit of knowledge"your answers were always lying on the ocean floor".
This makes me think of Atlantis, the lost city. Stories originally told of how it was sunk by the gods, which many ruins have depicted as alien life forms.
At the end, he decides to search for these answers and fight his fear of the unknown(Walk the plank! Your answers, were always lying on the ocean floor).
There is definitely another meaning to this though, since its started from the previous song, which voiced thier horror at the earths destruction, and some being that has waited for 1, 000 years to come back reaping its veangence for us destroying their home, this is the second part to it.