The Nihilim are what is assumed to be a species of interdimensional travelers. Their ability to pass through the third dimension (by presumably moving through the fourth), is inferred through the extremely rare relics they leave behind during travels: Atmos being one of the largest structures to ever remain in the third dimension.
How their technology works is entirely unknown, as the tech left behind is rarely ever fully in the third dimension, and bleeds into the higher dimensions, stalling all research.
LOGO has refused to share knowledge of higher dimensions beyond existing data. details: Access to data on higher dimensions denied.