The game is divided into small stages, each of which represents a certain area. As the game progresses, the player gradually moves from exploring individual rooms in a house out into the street and the areas beyond. Using the on-screen cursor, the player aims at and captures Elebits, extracting their energy (measured in watts). Levels in the Story Mode are completed when the player reaches a certain power (usually within some pre-defined time limit).

The player manipulates objects in the world in order to hunt for Elebits, using the Wii controller as a "Capture gun" similar to the Gravity Gun in Half-Life 2. As the majority of Elebits on a given level are hidden within or underneath objects, players must interact with the environment to reveal these hidden Elebits.

As more Elebits are collected during a given level, the area's energy is gradually restored. This causes dark rooms to become well-lit, and more importantly, allows various electrical appliances to be utilized. Once sufficient power is available, players can activate these appliances, such as computers, microwaves and electric toy-cars, which in return release Power-Elebits. Power-Elebits, when captured, slowly increase the strength of the "capture gun", allowing the player to lift and move heavier objects.