Cleopatra sends her advisor to investigate the death of a Roman soldier, a spy for Octavian that broke into the royal palace and was later murdered in the docks. The advisor starts to uncover a conspiracy against the Queen, with political intrigues and power struggles threatening the future of Egypt.
Mystery of Cleopatra is a hidden object game with adventure elements. As Cleopatra's personal advisor, the player has to search locations around Alexandria for clues about the murder. The screen shows a place from Ancient Roman times, with slots at the bottom displaying gray pictures of objects. The items have to be collected from the scenery by dragging and dropping them over their slot counterparts. In some places, certain portions of the scenery open up a number of circular spots with gray pictures, and the objective is to drag and drop the items inside them to perform an action or to complete a task.
Some of the puzzles take place on a separate screen, where objects and mechanisms have to be manipulated to solve them. These puzzles can be skipped at any time without penalty. The hint button provides information about the pending tasks, and the position of required items, but takes some time to recharge after use.