Secret Stones are key items that appear in Tears of the Kingdom.
Tears of the Kingdom
The Zonai were the descendants of gods, who brought powerful objects known as Secret Stones when they first came to Hyrule. These stones amplified the abilities of whoever possessed one. Rauru gifted one to the Hylian Sonia, and they used their abilities to become the first King and Queen of Hyrule. Soon after, Ganondorf killed Sonia and stole her secret stone, using it to become the Demon King.
Unable to defeat him, Rauru entrusted four stones to the most abled warrior from each of the four major regions of Hyrule - the Rito, Goron, Zora, and Gerudo. These warriors became the Sages who would use their power to fight against Ganondorf in the Imprisoning War. Though the Sages outnumbered Ganondorf, they were still unable to defeat him. Rauru sacrificed himself and used his abilities to keep Ganondorf locked Beneath Hyrule Castle, where the two remained for thousands of years.
Mineru, an expert on Zonai history, explains through memories that the stones can be used for draconification. This involves the person consuming the stone, which will transform them into an immortal dragon. This, however, will cause that person to lose everything that makes them who they are, and is considered to be a forbidden act.
In the present day, Regional Phenomena are affecting the major areas of Hyrule. At each area, Link finds someone from the region who has power that exceeds others like them. Together, Link uses their power to find a Temple in each area, and defeat a creature inside that has been causing the Phenomena. After doing so, the Sage of the respective region reveals themselves, and explains their part in the Imprisoning War. The Sage also says that the Sage of Time had come to them, and told them that Link would need the help of their race in the future, to which they readily agreed. To complete this promise, the Sage of old gives their secret stone to a present-day warrior, who becomes the new Sage.
The new Sages use their secret stones over the course of Link's journey to help him when he needs it most. This includes allowing Link to use their respective power whenever he needs it, through avatars that Link has been given. When Ganondorf attacks Link at Hyrule Castle, the Sages appear and defend him from the Gloom attack. When Link travels deep into the Depths to fight Ganondorf, the Sages appear and use their abilities to fight The Demon King's army, along with a creature from each Temple that has respawned. While Link is fighting Ganondorf, the Sages use their power to attack the Phantom Ganons that Ganondorf spawns.
Secret Stone of Light
A stone originally owned by Rauru, who obtained it at an unknown time. It amplified his power of light, which he used to defend Hyrule against a swarm of Molduga sent by Ganondorf. During the Imprisoning War, he used its power to seal Ganondorf away. When Zelda and Link travel beneath Hyrule Castle to investigate the gloom, they find the remnants of Rauru and Ganondorf. Rauru's hand falls off of Ganondorf, with his secret stone landing in front of Zelda. She grabs it, and inadvertently uses it to travel back in time during the Upheaval.
In the past, Zelda, as the Sage of Time, uses the stone while attempting to expand on her power over time and return to her own era. After the Imprisoning War, she realizes her purpose is to restore the Master Sword to its former state. Finding that draconification is the only option, she consumes the stone, and turns into the Light Dragon. After Link has defeated Ganondorf, Rauru and Sonia's spirits transform the Light Dragon back into Zelda once more. Afterwards, she is still wearing the stone around her neck.
Secret Stone of Time
Gifted to Sonia by Rauru before becoming King and Queen of Hyrule. The stone enhanced Sonia's power over time, which allowed her to use a Recall ability later passed down to Link by Zelda. One night, Ganondorf kills Sonia and takes her stone, using it to become the Demon King. After his defeat in the Imprisoning War, the stone stayed with Ganondorf as he withered away for thousands of years.
In the present day, Ganondorf reanimates and begins the Upheaval. The stone amplifies his power over darkness, which he uses to summon monsters and fill the Depths and Hyrule with gloom. Before his defeat at the hands of Link, he is insistent that he will destroy Hyrule at any cost, and consumes his stone. The process of draconification turns him into the Demon Dragon. After his eradication in the skies of Hyrule, the stone is no more.
Secret Stone of Spirit
A stone owned by Mineru, who obtained it at an unknown time. The stone allows her to separate her spirit from her body. The power becomes prevalent when, after the Imprisoning War, she is near death. She preserves her spirit inside the Purah Pad, which stays with a Steward Construct until Link obtains it thousands of years later.
When Mineru initially presents herself to Link, he builds a construct for her spirit to reside in. Her stone, however, lies in the Spirit Temple, so she cannot immediately inhabit the construct. After traversing the Depths and defeating a Seized Construct, Mineru uses the stone's power to enter Link's construct. Mineru gives Link the ability to use her construct at any time as the Vow of Mineru.
Secret Stone of Wind
Originally belonged to the Sage of Wind from the Rito, given by Rauru during the Imprisoning War. It is later given to Tulin near the end of the Tulin of Rito Village main quest. The stone amplifies Tulin's ability over wind, allowing him to send a large gust of wind in any direction. This power is given to Link as Tulin's Power of Wind.
Secret Stone of Fire
Originally belonged to the Sage of Fire from the Goron, given by Rauru during the Imprisoning War. It is later given to Yunobo near the end of the Yunobo of Goron City main quest. The stone amplifies Yunobo's fire power, allowing him to create a fiery roll that can be targeted into boulders or enemies. This power is given to Link as Yunobo's Power of Fire.
Secret Stone of Water
Originally belonged to the Sage of Water from the Zora, given by Rauru during the Imprisoning War. It is later given to Sidon near the end of the Sidon of the Zora main quest. The stone amplifies Sidon's water abilities, allowing him to create a bubble around Link that acts as protection. It will block enemy attacks, and can be used to attack enemies or dissolve sludge. This power is given to Link as Sidon's Power of Water.
Secret Stone of Lightning
Originally belonged to the Sage of Lightning from the Gerudo, given by Rauru during the Imprisoning War. It is later given to Riju near the end of the Riju of Gerudo Town main quest. The stone amplifies Riju's lightning power, allowing Link to perform a lightning strike wherever necessary. This power is given to Link as Riju's Power of Lightning.
- The music that plays upon defeating a boss and gaining access to a Secret Stone is a remix of the theme that plays when a stage is complete in Age of Calamity. This may be a reference to how the four Sages-to-be were all sucked into the new version of the past created by Terrako (with Tulin's presence being confirmed during the Guardian of Remembrance DLC) before later being sent back to their own time and timeline as more accomplished warriors, ready to take up the Sage mantle by the time Tears of the Kingdom occurs.
- However, this also plays when Mineru gains her Secret Stone, despite her not being present until Tears of the Kingdom.