An Antarctic Mystery follows Mr. Jeorling, a wealthy American naturalist whose research has led him to the remote Kerguelen Islands, located in the southern Indian Ocean. Jeorling begins his adventure on the Halbrane after being admitted aboard by the reluctant captain Len Guy, who believes the events in The Narrative of Arthur Gordon Pym to be true. In that novel, Pym persuades Len Guy’s brother, William Guy, to lead a voyage to the Antarctic. But the expedition ends in failure when William Guy, his crew, and his ship, the Jane , disappear under mysterious circumstances. Captain Len Guy convinces Jeorling to aid in the search for his brother, and the two embark on an expedition south to the Antarctic in search of the previous voyage’s survivors.

Despite the fact that Jules Verne’s work was published over fifty years after Pym , the events in the novel take place only one year after the disappearance of the Jane .