The game is a indirect sequel to The Legend of Zelda: Twlight Princess, taking place many centuries after it. When Princess Zelda is kidnapped and taken to the Underworld for her magic, her best friend Link goes on a quest to save her under the guidance of former witch Impa. Impa first tells him to go to the Master Temple to pull the legendary Master Sword out of it's stone. When Link returns with the sword, Impa is convinced he can save Zelda. She tells Link of three pearls scattered across the world, capable of creating a portal to the Underworld. After Link collects all three, Impa casts a spell on them and they create the portal. Impa warns Link that if he goes into the underworld he may never come back, but Link continues on for Zelda's sake. Not long after entering the Underworld, Link meets Midna who aids him because he reminds her of someone she had known long ago hinting at the events of Twilight Princess. After infiltrating the the demon king Gaonmu's Tower, Link and Midna find a weakened Zelda, and tries to escape with her but is confronted by Gaonmu. Link kills him after a brutal battle with a silver arrow given to him by Midna. Upon his evil soul being released from his body, the tower is reduced to rubble. Unable to escape in time, Link shields Midna and Zelda with his body from all the collapse. Zelda uses the last of her power to pull them from the wreckage. Midna tells them that a gate between the Underworld and Light world opens every 100 years for a few seconds and that it may be their only chance to leave the Underworld. After Link and Zelda make it through the gate, the game ends. The ending credits shows scenes of Link and Zelda growing up together, closing with Link and Zelda kissing for the first time.
- Master Temple: A temple created to keep the legendary Master Sword out of the wrong hands. The blade lays in it's depths.
- Light Temple: One of three temples created for the pearls that lead to the Underworld. It contains the Pearl of Light, and represents wisdom.
- Dark Temple: One of three temples created for the pearls that lead to the Underworld. It contains the Pearl of Darkness, and represents power.
- Twilight Temple: One of three temples created for the pearls that lead to the Underworld. It contains the pearl of Twilight, and represents courage.
- Gaonmu's Tower: The domain of a powerful demon lord where none dare to trespass.