The manga is not considered canon, so it can't really be considered a true prequel to Majora's Mask. Some have theorized that the Dark Tribe mentioned in Majora's Mask are connected to the Dark Interlopers mentioned in Twilight Princess, the latter of which we may learn more about in Skyward Sword.
Ducky took the words right out of my mouth. The manga is not cannon, but the story at the end of the book goes like this. It explains about a beast that lived in a deserted part of the world with no time or space. A legend said that anyone who were able to wear the beast's armor would be granted a wish and incredible power. Many humans tried to obtain it, but failed and were defeated by the monster. One day a traveler appears and speaks to the beast and shows him pity for the thousands of years he has spent alone in the space with no time. The pity he shows causes the beast to realize that he cannot leave the space and he begins to feel the hope of all the humans he killed. The traveler uses a drum to create rhythm and in turn create time in the empty space. The beast dances for three days and on the dawn of the fourth day dies and so does the world he lived in, the only thing left was his armor. The traveler sits down and carves the armor into Majora's Mask and says that beast's power is safe inside the mask and that he may now sleep forever.
Now, it is a nice story and the author clearly thought about the game when he wrote it, but it is infact, not true. but I thought I would share it with you anyway, in case you were curious. The story does not explain the origin of Fierce Deity or 'them'.
The origin story you want may be revealed to us all with the release of SS. Ducky beat me to it, but I believe that the Dark Interlopers are a group of evil-doers and that Majora's Mask may or may not have been a tool that they had the use of. We do know from in game that Majora's Mask was used by an ancient tribe for hexing rituals. The power of Majora's Mask may have been to risky for them to keep so they disposed of it, or the Happy Mask Salesman wanted it so bad that he stole it from them. That would make him avery brave man in my opinion. Because of the potential link between 'the ancient tribe' and 'the dark interlopers' (which would include beings like Ganondorf, Ghirahim, and Agahnim) I would not put it past the fact that the mask may have belonged to them at some point. Stolen by the Mask Salesman to be stolen by Skull kid? Potentially I think. Also, you cannot rule out the fact that Majora's Mask (the game/story) has the potential to be a dream, or Link's death story, ect. None of the other theories I have heard are to far fetched for me to throw them out completely. If this is really the case, then the mask has no origin at all. It is simply an evil that Link's subconscious mind thought up while he got lost in the forest and turned into a stalfos know as the Hero's Shade...getting off topic.
Out of all of this discussion though. I would really like to get more backstory on Fierce Deity. He was, in my opinion, epically cool and thrown in with no more story than 'his power may be as powerful and evil as Majora's' (that is not a direct quote at all, completely a paraphrase from what I remember of that cut scene). And as I make that point I go back to the fact that if Majora's Mask was used by the dark interlopers, then the potential that Fierce Deity's was as well.
My overall point though is I doubt we will get a 'Majora's Mask prequel' but we are more likely to get snippets of info here and snippets of info there. The closest we are going to get for right now lies in the plot of Skyward Sword. So we all will sit impatiently and wait *twiddles thumbs*