This album tells the legend of a ghost ship (an interpretation of The Flying Dutchman) from its beginnings. The album starts in the future, when a boat with an electronic communication device sails to the sea. The boat picks up signs of an eerie voice cursing its captain's name through the radio. Then a ghost ship comes across the sea. The sailors then remember stories about how people who saw that ship died in horrible ways. In track No. 3, in the same day of the sighting, later that night, the captain is haunted by the ghost of the seas. He kills his wife and daughter while sleepwalking and then kills himself with a shotgun. After that, it begins telling the story of Van der Decken and how he became the captain of an evil ship.
The album contains symphonic black metal although the vocals are kept clear. Parallels to Dimmu Borgir have been observed in the keyboard lines and the vocals' timbre. The structure of the songs has been described as "bulky" with many abrupt breaks, which is contrary to traditional black metal structures.
Death Came Through a Phantom Ship received positive reviews from Sputnikmusic and the German edition of Metal Hammer. The former observed that the band had even improved their instrumental qualities compared to their debut album Lammendam and recommended the new album for listeners new to the genre. Metal Hammer praised the diversity of the songs but was sceptical of their unusual structure.