- Link - The main and only playable character. His friendship (possibly relationship) with Zelda may or may not be strained over the course of this game.
- Zelda - The other main character. An incident leads to the leaking of a hidden truth Link may have been hiding from Zelda about his true side.
- Darunia - Link's friend and partner. He is traveling with Link to win back Zelda's trust and to discover the truth. Also the Fire Sage.
- Princess Ruto - Link's friend. She is curious about the "truth" that has strained and turned the course of Hyrule's destiny. Also the Water Sage.
- Saria - Link's friend. She is concerned about what Link has been hiding from the world for the longest time. Also the Forest Sage.
- Impa - Link's acquaintance, but he owes a few thanks. She is out to see if Link's secrets involve her or hurting Zelda in any way. Also Zelda's bodyguard and the Shadow Sage.
- Nabooru - Link acquaintance and the Spirit Sage. She believes that Link's journey is to try to erase everyone's mind in Hyrule, and is one of the antagonists.
- Rauru - Link's former friend who has passed away, but his spirit may provide answers.
- Malon - A girl who now owns Lon Lon Ranch, and also Link's friend. She has been looking after Epona for years.
- Epona - Link's horse who is now under the care of Malon. He is summoned when a song titled Epona's Song is played by someone it truly trusts.
- Master Sword/Sword of Lies - The Master Sword, but if the holder is not worthy, it turns into the Sword of Lies.
- Owl Horn - Blowing one of these multiple horns summons Kaepora Gaebora to take you anywhere. It only has 2 uses. Due to the Ocarina of Time becoming the Ocarina of Lies, this is the only way to summon Kaepora Gaebora.
- Epona's Flute - A flute acquired when finding Malon. Due to the Ocarina of Time becoming the Ocarina of Lies, this is the only way to summon Epona.
- Aqua Accordion - An accordion that summons the power of storms and water. It is the substitute for the Song of Storms.
- Ocarina of Time/Ocarina of Lies - The Ocarina of Time, and it turns into the Ocarina of Lies when a non-worthy holder possesses it. The notes are off-key, and the effects are reversed.
- Platinum Shield - Link's new shield.
The gameplay strongly resembles Ocarina of Time. The GameCube remote and the classic controller can also be used for the game. The controls on the GameCube remote and on the classic controller are the same as on the virtual console. The graphics are strongly, strongly improved from Ocarina of Time. Link can run faster, and Hyrule Field is a bit shorter. Link uses a shield now called the Platinum Shield.
In some parts of the game, Link must put the Sword of Lies/Master Sword in the pedestal to solve mysteries as a child.
The Sword of Lies is a version of the Master Sword that, while more powerful, holds the ghost of Ganon, who is trying to find a host body. The Ocarina of Lies is practically useless, as it hurts you in various ways when certain songs are used. However, it is a key item needed to prove some facts to the antagonists.