Beat the game with all of the Magic, Heart Squids, and upgrade items.
Extra Final Boss and alternate ending
Collect all twenty Dark Magic from the Cursed Cacklebats, then defeat the final Boss. A new cinematic will play, followed by a second phase of the Boss battle and finally an alternate ending.
Farming money
Go back to Tanline Temple and sneak back into Shantae's dungeon escape path. Follow the path until you come out to a bright room with a chest in the middle. Jump up from the chest's position to climb up to a room with pots on both sides. Break all pots, get all gems and go back down and exit through the door. Then, return and the pots will have respawned so you can reap gems as many times as you wish.
Game Clear
Beat the game.
GBA Level
Once you have the boot, on the first dungeon on Saliva Island, in the first room, ram into the little steps. You'll be able to go through a level from the first Shantae game, including GBA graphics (some bits that are used elsewhere in the game will still be in the 3DS style)
Main menu wallpapers
Complete the indicated task to unlock the corresponding wallpaper.
Wallpaper
How to unlock
100% Clear
Beat the game with all of the Magic, Heart Squids, and upgrade items.
100% Speed Run
Beat the game with all heart squids, dark magic, gear upgrades and fighting moves under two hours and thirty minutes.
Game Clear
Beat the game.
Speed Run
Clear the game in under two hours.
Make Infinite Money Quickly
To make infinite money, you need to have at least 130 gems (but preferably 260, or even better, 390). Then all you have to do is go to the item shop in Scuttle Town, and purchase the three-pack of Monster Milk (NOT the individual ones sold for 50!) for 130 gems. Once you have that, exit the item shop and head all the way left to the sobbing Town Mayor - who just happens to have an endless thirst for Monster Milk, and will happily pay you 50 gems for each one you give him. Since you bought the three-pack for less than the price of three individual Monster Milks, giving him all of your Monster Milk nets you a profit of 20 gems per 3 Monster Milks sold - meaning that once you can buy 9 Monster Milks, you'll be making 60 gems profit every single time you do it, quickly racking up the cash.
Pirate Mode
Complete the game once with any ending to unlock Pirate Mode, then select it when starting a new game. Playing in Pirate Mode gives Shantae all of the Pirate Gear from the beginning, allowing for new shortcuts and faster clear-times.
Shantae level
Obtain the boot, then ram the small steps in the first room of the first dungeon on Saliva Island. You will start a level from the Game Boy Color game, Shantae.
Short Boots Dash
Normally a long running space is needed to start a Boots Dash, this can be circumvented by using the circle pad and the d-pad in tandem. Start by moving the circle pad in one direction. Then press the d-pad in the opposite direction, letting go and pressing again as necessary. This will allow you to run in short spaces and execute Boots Dashes that were not intended, allowing you to sequence break the game heavily.
Speed Run
Clear the game in under two hours.
Use Boots Dash in small areas
Press the C-pad in a direction to begin a Boots Dash, then press the D-pad in the opposite direction, releasing and pressing it again as needed. This will allow you to use Boots Dashes in places that normally are too small.