To start the game, insert the cartridge into the Nintendo DS while it is off. Turn the handheld on. On it's menu screen select the Legacy of Ys panel, it should be at the top of the menu screen.
If you are playing on a Nintendo 3DS, insert the cartridge into the off console. Turn it on and find the cartridge's icon on your home screen.
Once the cartridge is loaded it will offer a selection screen where you can choose which of the two games you wish to play.
Title Screen
Both games start on similar Title Screens which offer the player several options.
- Load Game: A previously saved game can be restart from this option.
- New Game: A new save can be created through this option.
Once a game has been cleared on any difficulty two more options become available for that game.
- Time Attack: In this mode, you face the games bosses in sequential battles and are challenged to beat them as quickly as possible.
- Music Mode: In this mode you can select and listen to all the music files in the game.
Book II has an additional mode unique to it.
- Multiplayer: This mode allows you to play with up to 3 other players in a player in a competitive PVE game.
Status Screen
The Status Screen is visible at all times during gameplay such as currently equipped items and Adol's HP/MP. It's exact location is dependent on what control scheme you use.
- Equipment: Currently equipped items are displayed in two orders.
- Book I: Sword | Shield | Armor | Ring | Item | Book
- Book II: Sword | Shield | Armor | Magic | Accessory | Item
- HP: Adol's HP is constantly displayed as both a green health bar (game screen only), and as a numerical value (game & status screen)
- MP: Adol only gains magic and MP in Book II. It displays the same was as HP and can be found beneath HP bar and numbers.
- Level: Adol's current level.
- Next: The number of experience points Adol needs to reach the next level.
- Gold: The current amount of gold possessed.
- Hint: A small text hint is displayed to help players figure out what needs to be done.
- Map: A map shows the current area and Adol's position in it.
Menu Screen
The Menu Screen can be reached during gameplay by pressing the 
. It consists of four windows which which can be cycled through.
Window 1: Equipment
All owned equipable gear can be found here. Each type of equipment has its own section. When an item is selected the upper screen shows more detailed information on it. Currently equipped items are marked by a blue outline. To change equipment highlight the desired gear and press 
or tap it with the stylus.
Window 2: Items
Miscellaneous, key, healing, and magic items are displayed in this window. Equipping items works the same as in the equipment screen. Some items are passive and their affects are immediate upon exiting the menu screen, other items will have to be activated. The method of activation is reliant on the control scheme used.
Windows 3 & 4: Save and Load
These windows allow you to save and/or load other save files. Loading a save file without saving the current one will undo any changes/progress made to the current save file.
Options Menu
The Options Menu can be accessed by pressing the 
during gameplay. This menu allows you to change your current control scheme. You can also quit the game and return to the title screen from this menu.
Difficulty Levels
When selecting a new game you are given the option of selecting what difficulty you wish to play on. Once chosen you will be locked into that difficulty setting for that save file.
- Very Easy: Monster damages and health are reduced and your attacks increased.
- Easy: Monster damages and health are reduced.
- Normal
- Nightmare: Monster damages and health are raised, your attacks are reduced, and you do not regain health automatically when inactive in the field.