Majora’s Mask 3D picks up immediately after Ocarina of Time. Link, our protagonist, has just saved the world as an adult before being sent back in time seven years. Suddenly, he has the body of a child, and nobody remembers any of his adventures except for his fairy friend Navi, who has disappeared.
Link goes looking for Navi, but while he’s riding through a mysterious forest he is attacked by the mischievous Skull Kid, who is wearing Majora's Mask. While chasing Skull Kid, Link arrives in the parallel world of Termina, where every person he meets looks exactly like someone he met in Ocarina of Time. Stranger yet, the moon is falling, and expected to crash into Termina in 72 hours’ time.
Majora’s Mask 3D is spent reliving those 72 hours over and over again. On each three-day cycle, Link meets more people who are suffering, usually as a result of the Skull Kid or of the impending apocalypse. When he helps someone, Link receives a mask which gives him some special ability. But every time he restarts the cycle, the people he helped go back to being in trouble, and nobody can remember who he is.
In order to complete the game, Link must defeat four temples and then go to the moon to battle Majora's Mask. The mask is possessed, and it was taking advantage of Skull Kid in order to bring about the end of the world.
There are a number of differences between the original Majora's Mask and this remake. These include:
- The bomber's notebook is expanded and more detailed.
- The boss battles have been redesigned.
- There is a new hints system.
- There are more save points, and they create permanent save files.
- The dual screen allows for maps to be displayed at all times.
- Two fishing holes were added: one by the swamp, one by the ocean.
- The Stone Mask and the Giant's Mask have been relocated.
- Some pieces of the Great Fairies have moved to be easier to locate.
- The Song of Double Time can now move you forward to a precise time later in the day.
- The Song of Soaring is now acquired earlier in the game.
- The sword is no longer required to access save statues.
- The bombers only need to be caught once before you acquire the bomber's notebook.
- The Gyorg mini-dungeon on the moon has been redesigned.
- You can equip a mask immediately, even while wearing a transformational mask.