Edwina Margrave receives a letter about the "Aurora Dusk", a derelict ship found offshore that belongs to her family. She was raised in an orphanage, never meeting her real parents. Since the boat is hers by inheritance, she decides to travel to the coastline and inspect it personally to uncover details about her family history.
Like its predecessor, Margrave Manor 2: The Lost Ship is a hidden object game with adventure elements. Most of the time, the objective is to find and click on all the items listed at the bottom of the screen, on locations cluttered with assorted paraphernalia depicting the many decayed rooms of the abandoned ship. Some of the objects are stored for later use, on separate screens where the list is replaced by inventory slots containing them. In these sections, the goal is to drag and drop the inventory objects on parts of the screen to solve puzzles, like using a key to open a padlock.
A separate puzzle screen comes up when clicking on certain parts of the scenery. These puzzles usually have pieces and mechanisms that must be manipulated directly to be solved. There are implementations of recurring mini-games of the genre, like jigsaw puzzles with letters and maps, and a spot-the-differences game with the screen split in two similar images. Other challenges include a Tangram game with jewels, a Pipe Dream clone, a puzzle featuring pieces with pentominoes shapes and similar games. The hint button at the bottom interface highlights the exact position of one of the required objects. Extra hints are added automatically after several minutes. In the freeplay mode, previously visited locations can be accessed again to collect all the items.