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.

High school freshman Hiromi joins the tennis club because of her admiration for Ryuzaki. Ryuzaki is a senior, who's the best tennis player on the team and also nicknamed "Ochōfujin", ("Madame Butterfly"), because of her elegance on the tennis court. However, the new coach, Jin Munakata, wants the inexperienced Hiromi to play in a forthcoming tournament.