The Shadow Cube is an ancient artifact that is said to have unlimited power. The Cube is able to corrupt people and grant them powerful abilities, including psychic abilities and mind control. The Cube can not however corrupt people that have a strong will, like Mario, nor can it control a deceased person. The Shadow Cube, in Story Mode can unlock areas in the overworld covered in Lord Byrinth's dark energy.
During Story Mode, Lord Byrinth tries to take back the Shadow Cube from Mario so that he can regain his dwindling powers.