Master martial artist Masahiro Kai is a shadow of the champion fighter and trainer he once was. After his protégé was slain in a no-holds-barred, underground fight by the incomparable Chang Lee, Kai slips into a numbing alcohol-induced stupor to try to forget the past.

The plot of Marine Express can be described in two parts. The first part focuses on the people boarding the train and the problems they encounter on it. The second part takes place after the train has stopped at its half-way point, an island that used to be home to an ancient civilization millennia ago and has its fair share of secrets.