Matrix Madness exercises and evaluates the player's pattern recognition skills by posing a series of 3x3 grid puzzles, filled with abstract graphical shapes except for a single empty space. The player must grasp the logic behind the arrangement and select the right shape to fill in the blank, scoring depends on reaction time and on the number of guesses taken.

The puzzles come in three difficulty levels, which determine the complexity of the patterns (and the number of optional answers available). After ten questions a final score is given, which can be compared with that of a hypothetical "good player" to assess the player's mental prowess.