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.

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. This most often requires using the shape abilities together to maneuver them appropriately. The goal in 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. Though the shapes themselves cannot be heard, the narrator describes the personalities and thoughts of each shape as the game progresses. When the player has access to two or more of these shapes, they can freely switch between them, controlling one shape at a time. 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 they may have other abilities, such as being able to float on water. Each entity is represented by a simple coloured shape the game's eponymous character is a simple red rectangle.

Thomas Was Alone takes place within a computer mainframe, where some unspecified 'Event' has caused several artificial intelligence routines to run out of control and gain personality. In Thomas Was Alone, the player manipulates several rectangular shapes across a platforming environment, using their unique abilities, such as floating in water, to aid the other shapes.

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