I think this is about a relationship that is going worng, no matter what they try. The voice is desperately trying to hold on to what they've had, but he can't "Need you like water in my lungs."
Then when its like "Your tongue is a rudder..." and that bit its like saying that what ever happens it is down to what is being said.
When it says "You know that you are not alone" I think he means that the gril knows that he will always be there for her.
Basically I think Jesse is using a boat and a ship wreck as a metaphore for a relationship falling apart (the boat is the relationship)

Could be wrong though, could be a load of bollocks that seems to fit!