The silent player-protagonist is the twelve-year-old nephew of the brilliant but peculiar Professor Fitz Quadwrangle (voiced by John de Lancie).

The experiment goes awry, causing Quadwrangle to become trapped in a pocket dimension with a loss of memory of what went wrong before, but able to watch and communicate to the protagonist.

The protagonist also gains help from IKE (Interdimensional Kinetic Entity), a small alien creature that Quadwrangle had adopted as a pet during his travels.

Most puzzles require the player to manipulate the room and objects within it using four different dimensions which impart unique physical properties to the world.

Kim Swift was one of the developers of 2007 video game Portal by Valve, an extension of her student team project Narbacular Drop from the DigiPen Institute of Technology.

[8] Swift's goal with Quantum Conundrum was to create a title that would have broad appeal to a wide audience but still be challenging to hardcore players.

[8] Weekly playtests were done at Airtight to assure playability throughout the development process, in conjunction with tests performed by Square Enix.

The use of skewed angled and curved surfaces helped to guide the player's eye, while also giving a "quirky and fun" look to the environments.

[8] Lighting and shadows were critical towards this aspect, using both to highlight features of rooms and point players towards specific elements.

Bob Mackey of 1UP.com gave the game a B−, but stated: "But even in a vacuum, Conundrum's brilliant moments are hampered by an inconsistent world, an emphasis on performance rather than ingenuity, and a level of humor that wouldn't be out of place at your local pre-school."

"[19] IGN gave Quantum Conundrum an 8/10, praising the clever puzzles but criticizing "lack-luster" environments and the game's ending.