Thomas Was Alone takes place within a computer mainframe, where some Event has caused several artificial intelligence routines to run out of control and gain personalities. Each entity is represented by a simple colored shape; the game's eponymous character is a simple rectangle. Each shape has unique abilities; while all shapes can move left or right across platforms and perform jumps, the height of these jumps may be limited by the shape, or may have other abilities such as being able to float on water. When the player has access to two or more of these shapes, they can freely switch between them, controlling one shape at a time.
Though the shapes themselves cannot be heard, the narrator describes the personalities and thoughts of each shape as the game progresses.
The goal on each level within the game is to direct the shapes to exit points specifically tied to each shape, so that they all simultaneously occupy this exit. This most often requires using the shape abilities together to maneuver them appropriately. A shape that cannot jump very high can be helped by creating a staircase from other shapes so that the shape can reach a higher platform, or the shape that can float can ferry the other shapes across water. A shape can be lost to several hazards, but it will reappear at the start of the level, or at a checkpoint if the shape has passed such a point.
There are ten sets of levels, each introducing a new character, with about ten levels within each set.