The game is played entirely with the mouse in the case of the PC version (point-and-click). The cursor is contextual, meaning that it will change automatically to actions such as "Talk to...", "Pick up...", and so on, depending on the object (and state of the object) it is hovering over at the time. Item labels may be toggled at any time.
The game is divided into eight chapters (whereas the first and third Gabriel Knightgames [the second game, The Beast Within, has a structure similar to Gray Matter] were divided into "days"). Each chapter requires completion of certain objectives. Bonus objectives are also available for every chapter but are not required to advance the main story.
Puzzles include riddles, word games, visual puzzles, mazes, and magic tricks. As an aspiring magician, Sam often adapts tricks out of her magician's handbook to the situation at hand. The tricks vary from creating misdirection to using gimmicks or taking or planting objects through sleight of hand. If each required step is not performed correctly, the player has the opportunity to redo the trick from the last correct step.
The player controls Sam for most of the game, alternating to Professor Styles at certain moments in the story. The gameplay is the same for both characters, albeit with access to different areas.
