Lyric discussion by defunct 

I always thought it was about drugs. The ship being the drug that keeps him afloat:

"You'd better think about it, I just can't live without it. So, please don't take my ship from me"

-I take that as some type of intervention to try to get the person off of drugs.

"I'm your captain, I'm your captain, Although I'm feeling mighty sick. Everybody, listen to me, And return me, my ship."

-The intervention works so he tries cold tuckey but withdrawal makes him sick and he feels like he is drowing so he wants his drugs/"ship" back.

"I'm your captain, yeah, yeah, yeah, yeah"

-He relapses and goes on a massive binge.

"I'm getting closer to my home (to fade)"

-Either he is OD'ing and dying, or he feels at home tripping.

That's just my take.

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