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.

It seems that Lum's grandfather made an agreement that should he have a daughter, she would be married to a traveling merchant that he met. Now, the merchant has come to collect due. Ataru is tricked into thinking that Lum wants to leave, and so, in a moment of anger, says he hates her. Arguments erupt, and Lum decides that she must know the truth of Atarus feelings. As for all the questions of importance for the Onis, a game of tag begins, one that Ataru can win simply by telling Lum I Love You. However, in the end his pride may end up dooming him. So begins the series of events that will at long last decide the future and fate of Ataru and Lum.

A group of students from the Cosmo Academy are about to take their final exam: surviving for over fifty days in a derelict ship. But when they arrive, they discover that instead of ten students, there are eleven. One of them doesn't belong there...