I'm not sure if it is ever fully explained, but I know that a couple decades ago when I watched it, I really enjoyed it an it stuck with me. There is also Cube²: Hypercube which involves time distortion and parallel dimensions and also Cube Zero which shows the side from the ones organizing the cubes.

Both sequals are mostly riding the success of the 1st and aren't as good but I remember that I still very much enjoyed them also.