Brainpipe: A Plunge to Unhumanity takes the player on a trip through ten hypnotic stages where the steering is done using a first-person perspective through tubes with hypnotic colours. The game is shown through a wire-frame iris that becomes smaller when the player takes damage. When one more hit will cause the player to die, it becomes very thin and turns red. To complete a level players need to avoid objects and collect glyphs for bonus points. Every tenth glyph is a major one that looks different than the rest. Grabbing it earns the player more points and a level achievement. At level 10 this wins the game and provides a new form, an alien monster pic, and a special badge on the high score list.

The music syncs with the rhythm, movement and speed of the levels and the graphics are altered accordingly. During levels, the gameplay usually becomes faster, making it harder to dodge objects. To compensate, a button can be used to slow down time to get past obstacles with precision. The game's controls are very straightforward, only steering is needed, using the mouse, a joystick or a gamepad.