In the process of doing something involving their fancy gateways they accidentally damaged either the OS or memory in storage. This left blackholes scattered everywhere showing where the damage had physically manifested in their world. The whole plot of Fez is a bug fix program being activated to find all the missing data in the form of cubes to restore the OS/missing memory bits. Getting an incomplete number of cubes results in the Universe glitching out before doing a system restore, getting all of them refreshes the Universe in a now stabilized state where it isn't in danger of crashing.
The natives living in Gomez home village live in ignorance because the remaining leaders were convinced further multidimensional tampering could break the universe entirely. As such they took everyone they could find and intentionally set the subsequent generations up to have no knowledge of the third dimension. This was the best they could do to prevent an apocalyptic event. However they weren't aware that ongoing degradation because of the existing damage was slowly dragging it toward collapse regardless which resulted in Gomez being selected to fix the situation.