The Protagonist is the silent protagonist of Quantum Conundrum. He is the 12-year-old nephew of Professor Fitz Quadwrangle.
He is sent to stay with Quadwrangle, who is unprepared for his arrival as he is presently working on an experiment. The experiment goes awry, causing Quadwrangle to become trapped in an unknown place with a loss of memory of what went wrong before, but able to watch and communicate to the protagonist. The results of the experiment leave portions of Quadwrangle Manor in flux between several alternate dimensions with varying properties. Quadwrangle guides the protagonist to acquire a glove that can tame these fluxes so he can then safely travel through the labyrinth of rooms to reach three separate power generators and restart each, which Quadwrangle believes will allow him to escape his imprisonment. The protagonist also gains help from Ike, a small alien creature that Quadwrangle had adopted as a pet during his travels. As Quadwrangle guides him, he tries to recall the exact events leading to the current situation.