The game starts with a little story with Zelda and Link.
Zelda is worried about the seal is messed up so she wants to check on it, but as soon as she steps up to check the sword, it moves a bit. Then Vaati appears and kidnaps Princess Zelda. Vaati tells Link what his plans are and where will he be hiding, which is in Vaati's Palace. Vaati flies up and knocks out Link with a strong wind. Link wakes up and finds himself by fairies. They tell him he needs to go to three areas and collect enough rupees for the great fairies to show the path to Vaati's Palace, but he can't go alone: he will need the power of the Four Sword. So he pulls the sword and from one Link he becomes four Links. Onward they go for this exciting adventure.
In the DSi version, there are three doors you can unlock by getting three types of keys: Silver Keys, Golden Keys and Master Keys.