The current explanation goes that it was inspired by Shakespeare's "Hamlet". Prince Hamlet swore vengeance on King Claudius for murdering his father, the former King, and then marrying his mother, still Queen. Hamlet's famous Soliloquy was the passage in which the conflict in Hamlet's mind is detailed, and the second verse of "Pull Me Under" coincides pretty thoroughly with it. The very end of the song James can be heard singing this line from Hamlet:
Oh that this too, too solid flesh would melt"
Furthermore, after seeing the video, in an interview, Portnoy said "Who the hell was that wolfman guy in the video anyway? We had written it based on something else entirely". Portnoy noted that while Moore did not write PMU about Hamlet specifically, he
did write PMU about what Hamlet was about. Same themes, ideas, etc.
Seas increase and then fall again" refers to the "To be or not to be" solliloquy -- more specifically "to take arms against a sea of troubles and by opposing end them" and "to suffer the slings and arrows . . . " This sollioquy clearly outlines Hamlet's contemplation of suicide and his fear of being sent to hell for it. Additionally the song lyric states ,"Watch the sparrow falling
Gives new meaning to it all." This refers to the scene where Hamlet tells Horatio that if it is time to die, than so be it --"there is such prophecy in the fall of a sparrow." Finally, the lyric states,"I’ll take seven lives for one/
And then my only father’s son." This refers to Hamlet taking, through his tragic flaw, the life of Polonious, Ophelia, Claudius, Gertrude, Laertes, Rozencrantz, and Guildenstern -- seven total lives and then his own. The song is littered with references to Shakespeare's Hamlet and the theme of death found in the play.
P.S. I am an adjunct professor of English and a huge DT fan!