Unlike the PC version, one did not have to pause gameplay to to check the map, hints or look in the encyclopedia. These features were always available on the GamePad in the Wii U version, simultaneously with gameplay.

Inspired by the Miiverse interface, one could take notes and jot down puzzle ideas and solutions without having to use actual pen and paper. The left stick was used to walk, and to look around and find things to interact with one would point and move the GamePad with very relaxed and subtle motions. It was very reminiscent of using the Wii Remote to point at the TV, or mouse controls on a PC.

Unlike the PC-version, which used cursor controls to interact with puzzles and contraptions, each puzzle used custom motion controls. For puzzle objects which involved spin or rotate, one would physically rotate the GamePad. The GamePad rumbled and made tacticle sounds to mimic the object, as if you were holding it in your hands.

The Wii U GamePad was also used for several fourth-wall breaking puzzles. One of these puzzles involved one of the creatures hiding inside the encyclopedia, breaking the actual page and text in which it appeared.