Glitches in Majora's Mask 3D
Fierce Deity Link Anywhere
In order to perform this glitch, you must have obtained all masks, including the Fierce Deity's Mask. To perform the glitch, you need to have an item which can be used anywhere in the X button slot and the Fierce Deity's Mask in the Y button slot. Then go into first person perspective and open up the items screen, swap the X and Y buttons around so the Fierce Deity's Mask becomes highlighted. Afterwards, pressing both the Y button and the Y slot on the touch screen allows the mask to be worn. Opening any door while wearing the mask crashes the game.
Fierce Deity Link Anywhere 2
In order to perform the glitch, you must have obtained the Camera, the Hookshot, and every mask. To perform the glitch, go to the place you want to activate the glitch, and equip the Hookshot to Y. Then use the camera, and while using it, swap the Hookshot with the Fierce Deity's Mask, and press L and Y at the same time. You will now be Fierce Deity Link.
To undo the glitch, just wear another mask.
Fall Through the Ground
This glitch is relatively simple to perform. Link must enter East Clock Town and climb the stairs at the northern end that lead to the roof of Latte. He must then jump across the stone pillars that are on either side of the East Gate, then across the targets above Honey and Darling's Shop, eventually ending up in a fenced area above the Shooting Gallery, where a Silver Rupee can be found. There is a gap in the fence for easy exiting, and if Link stands on its extreme left edge and jumps diagonally, toward the stairs leading to South Clock Town, he will fall through the earth as the screen fades to white. He will then end up in South Clock Town as though he had gone down the stairs normally.
Fall Through the Ground 2 (Simple)
This glitch requires the Fierce Deity's mask and the ability to use it outside of boss battles. (See above) Go to Great Bay Coast, there is a wall between the coast and the few houses. This wall meets the rock wall on the right (If you used the Song of Soaring). Have Link climb on the wall here, slowly walk off. The deity will fall off, grab the ledge then fall and restart the area.
Transformation During a Cutsene
To perform this glitch, Link has to be in Goht's room, with the Fire Arrows and any transformation mask equipped. Right after shooting the Fire Arrow at the ice cube containing the boss, press the button with the mask. If timed correctly, the cutscene will activate and play just like it normally would. However, when the boss roars, the cutscene will abruptly stop and Link's transformation will take effect. The camera will stay focused on Goht, but the screen will dim and the visual transformation effect will be partially visible in the corner of the screen, as well as Link's yelling audible. The cutscene will then resume, and Goht will run over Link in his current form.
A Forward Backflip, also known as a Gainer, is a returning glitch from the original Majora's Mask. In order to do this glitch, you need to have access to Deku Link. The glitch can be performed in the First Cycle, and can be used for sequence breaking there. A good place to practice this glitch is at the slope leading up to the platform with the stairs to the roof of the Clock Tower. To do the glitch you need to perform a Backflip, then L-Target again on the next frame. Deku Link should grab the ledge leading to the roof of the Clock Tower. To get an idea of what you need to do, L-Target, then press the Home button. Press the Home button again, and mash down, A and the home button. You won't be able to see it, but you have begun a Backflip on that frame of gameplay. Exit the home menu, and hold L to re-target. Deku Link should grab the platform. This glitch can be used at various other locations, too, such as near the Silver Rupee Chest in East Clock Town (use Zora Link) and at the fence to the Deku Scrub Playground.
Enter Mountain Village without Hero's Bow
There is a slope added to the wall leading to the ice blocks. Testing confirms that it was not present in the N64 version. You can side-hop onto it and bypass the ice blocks by carefully traversing the slope.