Junkichi is the son of a rich landlord, while Koyuki is the daughter of a poor lumber worker. The mismatched pair soon finds love, and against his father's wishes, Junkichi decides to run away with Koyuki to start a new life. But when Junkichi is called off to war, they make a pledge to sing the song of engagement everyday until they are able to reunite

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.