(This was written by Hylian Dan on www.zeldauniverse.net. It’s one of the best theories I’ve read, so I’m sharing it here.)
Shigeru Miyamoto once stated in a Nintendo Power interview that the Zelda team’s primary goal for Majora’s Mask was to “present something which is very mysterious”. The game invites the player to act as a detective, to investigate the secrets and troubles of the people of Termina, and of Termina itself, and to heal them in the end. Though the central story of a troubled imp using a cursed mask to try to cause the moon to crash into Termina may seem fairly straightforward, many subtle details in the game add layers of darkness and complexity to this tale.
One example would be the implicit story of the Deku Butler’s son. Upon being transformed into a Deku Scrub, Link finds a strange tree that resembles his present shape and seems to be crying. Later, Link meets the Deku Butler, who is reminded of his absent son when he sees Link’s Deku Scrub form. At the end of the game, the Deku Butler is seen crying before the strange tree. Though the game never bluntly states it, it is clear that Majora’s Mask forced Link into his Deku form by stealing the soul of the Deku Butler’s son, leaving an inanimate tree in his place.
While I was recently replaying Majora’s Mask, I noticed a number of subtle details that seemed to penetrated the mystery of the game and led me to a shocking discovery. It occurred to me that the moon might not be falling just because of the unfortunate actions of Skull Kid. As its name implies, the world of Termina evidently has been destined to end ever since the early days of its dark history. Subtle details in the game indicate that the evil acts of Termina’s people had brought about the impending apocalypse. It’s all tied to the Stone Tower.