Looks like we're getting into Zelda theory! Alright, so:
Majora's Mask // Fused Shadow
The former was created by an ancient tribe in Termina. The latter was created by an ancient tribe in Hyrule. The Hyrulean tribe, referred to as the "Dark Interlopers" used dark magic to try and seize the Triforce. This dark magic took the form of the Fused Shadow, a weapon of great power the likes never before seen. They were banished by the Light Spirits (probable reincarnations of the ancient Water, Thunder, and Fire Dragons) to the Twilight Realm, a prison realm created by the Goddesses. Upon their imprisonment, the Fused Shadow was split into four pieces: one was hidden in the Forest Temple (Deku Tree), one was hidden in the Goron Mines (Death Mountain), one was hidden in the Lakebed Temple (Lake Hylia), and the last was sealed within the Twilight Realm, to ensure there never be a reunion of the four. There, the Dark Interlopers transformed with time into the Twili.
In Termina, we have an unknown tribe that may or may not have been affiliated with the Ikana. The Ikana were a people who bolstered a kingdom in ancient times, now in ruin due to a conflict with the Garo, as well as [possible] civil war. This ancient tribe, like the Dark Interlopers, created a hexing mask called Majora's Mask. Majora was an unknown entity, perhaps a god to them. Not much else is known about this tribe, but considering everything in Hyrule has an equivalent in Termina, the creators of Majora's Mask were most likely Terminan counterparts to the Dark Interlopers, and just as the latter were banished to the Twilight Realm, so too might the mask's makers have been eradicated from Termina. Where they have gone—who knows. Perhaps the Twilight Realm—an alternate parallel world—might parallel Termina just as it does Hyrule. Maybe the Twili are a joint race of the Dark Interlopers and the Mask Makers. Or perhaps a different fate fell upon the Mask Makers. Perhaps they were the Ikana and both civil war and invasion destroyed them.
My two cents on the subject.
It's been said before that regarding the timeline 'it would be best if those things didn't mather to the fans'. Guess Zelda fans are just being hard-***** and got what they wanted in the end. 
