Majora's Mask 3D is the 2015 Nintendo 3DS remake of the 2000 Nintendo 64 game, made by Grezzo, the studio behind Ocarina of Time 3D. It goes much further than OoT 3D did: saving works differently, the Song of Double Time is more precise, the Bombers' Notebook was rebuilt, the bosses were redesigned, and there are two new fishing holes and a seventh bottle. Sections marked New are not in the Nintendo 64 version, Changed means it works differently, and Gone means it was removed.
Saving
ChangedOwl Statues save for good. Just walk up and check one; you no longer have to hit it with your sword. Playing the Song of Time no longer saves, so save at an owl before you reset the three days. Some Owl Statues have moved.
NewQuill Statues: extra save points all over Termina, including inside dungeons. You can save at them but can't warp to them with the Song of Soaring.
ChangedThree save files instead of two, and after the credits you can save and start again from the Dawn of the First Day with all your masks, including the Fierce Deity's Mask.
Time and the Notebook
ChangedSong of Double Time now lets you choose the exact hour to skip to on the current day.
ChangedInverted Song of Time slows time to half speed (it was a third on the Nintendo 64).
ChangedBombers' Notebook: the Happy Mask Salesman gives it to you, not the Bombers. It has more entries, a schedule screen, a list of ongoing, rumored and finished events, and you can set an alarm so Tatl reminds you when something is about to happen. The Bombers tell you rumors that go into it.
ChangedThe clock is now a bar across the touch screen showing all three days and the minutes.
Controls and Masks
NewTouch-screen items: X, Y and two touch-screen slots, with the Ocarina and Pictograph Box on their own buttons. Fire, Ice and Light Arrows are separate items, so you can equip more than one type at once.
ChangedZora Link swims more slowly by default, which makes tight underwater tunnels easier; the old fast swim is now part of the electric barrier and uses magic. His boomerang fins come back instantly when you press B again.
ChangedDeku Link has to build up speed before he can skip across water, and a marker shows where he will land when flying from a Deku Flower. Goron Link curls up with one press of A and uncurls with another.
New Motion controls for looking around in first person, and full camera control with the New Nintendo 3DS's second stick or the Circle Pad Pro.
Bosses
Changed Every boss now has a new weak point in the form of an eye, and some are fought differently, with a second phase. Odolwa, for example, can be stunned with Deku Nuts while flying from a Deku Flower. You can also re-enter a boss's room once you have fought it, even if you lost.
New Side Content
NewTwo Fishing Holes, on the Road to Southern Swamp and at Zora Cape. See Fishing Holes.
NewSheikah Stone: as in OoT 3D, it plays hint videos, and it can also show photos of where many Pieces of Heart and Stray Fairies are.
Things That Moved
ChangedKoume's Target Shooting now gives a bottle, and the chest beneath the graveyard that used to hold a bottle now holds a Piece of Heart. See Heart Pieces.
ChangedThe bank is in South Clock Town, in the back of the Clock Tower.
ChangedGreat Fairies: the Great Fairies of Power and Wisdom have swapped places, along with their rewards, and three Stray Fairies in Woodfall and Snowhead Temples are in new spots.
Changed The Bombers hide in all five parts of Clock Town, Shiro is now at the Pirates' Fortress, and the frozen Goron Elder is near the first of the Twin Islands.
Changed Magic Beans cost 100 Rupees at the Trading Post, and Powder Kegs cost 20 Rupees instead of 100. The Giant Wallet can be won on any of the three days. The Mask of Truth now reveals hidden grottos.
Graphics
Changed Rebuilt models and textures in the style of Ocarina of Time 3D, with stereoscopic 3D, running at 30 frames per second instead of 20. South Clock Town has a bigger plaza, and most cutscenes are shorter after you have seen them once.