The 'Aliens' in FEZ are referenced throughout the game, no one has a full idea on what they are but the most popular and likely story is:
The Zu lived in a 2D world until one day aliens came down giving them the power to see the world in 3D (Fez). They left only a few traces such as the Skull Artifact. There are also giant floating statues of them in the last zone of Fez.
The 'Aliens' can be seen on many wall carvings left by the Zu.