- "This place has an oddly organized and quiet feel to it... but there is something ominous about it."
- — Midna
Link is forced to seek out the legendary Blade of Evil's Bane, the Master Sword, in order to break a curse placed upon him by Zant, the Usurper King of Twilight. After working his way through the Faron Woods and battling a forest spirit known as the Skull Kid, Link finds himself in the ruin of a grand, ancient temple which turns out to be the ruins of the Temple of Time, the home of the Master Sword. After solving the puzzle presented by the statues meant to guard the Master Sword, Link finds the Blade of Evil's Bane in a solemn grove that was once the grand chamber of the Master Sword. After the sword breaks the curse on Link, the hero pulls it from the Pedestal of Time so that it may once again combat evil at his side.
Later in the game, Link is in search of an "ancient grove", one of the locations said to hold one of the lost shards of the broken Mirror of Twilight. He deduces that this grove is none other than the Sacred Grove. Returning to that hallowed place, Link inserts the sword into the Pedestal of Time for a brief moment, causing a statue guarding the main door of the former temple to vanish. Upon opening this door, the Door of Time, Link finds himself teleported back through time's flow, into the mighty Temple of Time as it had stood in the days of his forebearer, the Hero of Time. Going forth to the chamber of the Master Sword, he stabs the Pedestal of Time once more to reveal a hidden staircase leading up to the window right behind the Pedestal of Time, the same window which Navi disappeared into at the end of Ocarina of Time coincidentally. This turns out to be an illusion hiding another doorway. Proceeding through this doorway, Link enters a whole new area of the temple. Inside the temple, he finds a magical rod called the Dominion Rod which had been left behind by the Oocca race. This rod allows him to bring certain statues to life and control them. Eventually, he comes upon the chamber of a gigantic arachnid called Armogohma and uses the Dominion Rod to destroy the creature. With Armogohma's defeat, Link reclaims the shard of the Mirror of Twilight that had been sent into the temple by Zant.
During the end credits, members of the Resistance are seen exploring the ruins of the temple.
The dungeon consists of eight floors, built somewhat like a tower. The main objective of this dungeon is to locate a statue that can open a large door leading to the boss. The dungeon is infested with spiders and includes electrical fences. Many of the puzzles involve weight, whether it be pushing down Foot Switches with small statues or getting across a giant pair of scales. It should be noted that once Link finds the statue, navigation through the dungeon is slightly easier, as the statue wields a large hammer that can be used to smash gates and other obstacles.
Some suspect the new portion of the temple is actually the Temple of Light spoken of in Ocarina of Time that sits at the heart of the Sacred Realm. This is supported by the constant appearance of the Light Medallion's symbol in the temple. Also, the windows in the new part of the temple show an endless expanse of white sky, similar to the 'golden' sky described in the Book of Mudora's description of the Sacred Realm. It is also possible that it could be the Tower of the Gods from The Legend of Zelda: The Wind Waker. None of the forest which ought to be outside the dungeon is visible through the windows, though this is likely due to the temple being in the past, when there was no forest surrounding it.
The stone wall surrounding the entrance to the Master Sword Chamber (where the Door of Time was located in Ocarina of Time) is inscribed with Hylian scripture, reading "Sanctuary, Master Sword, Copyrod, Stone Statue". This suggests that the expanded part of the temple which serves as a dungeon in Twilight Princess could have been built long after the era of The Hero of Time, to house the Dominion Rod ("Copyrod") deep within one of Hyrule's safest places; The Temple of Time (or Light, as previously mentioned).
Both the Dominion Rod, which is the main item of the Temple of Time, and the Command Melody, which is learned in the Tower of the Gods, are used to control statues in their respective dungeons. The similarity between these two aspects of the dungeons may suggest some sort of relation between the two. Also, the Tower of the Gods and the Temple of Time both have a Darknut for a mini-boss.
Instead of the theory that the Sacred Grove reached the abandoned Temple of Time and Castle Town over the years, it is also possible that the Temple of Time was magically relocated to the Sacred Grove by the Goddesses or the Sages, for the purposes of protecting the Sacred Realm and the Master Sword from evil forces by hiding the Temple in an extremely remote area. By placing it in a secret place, the Temple of Time would be left untouched for decades, where it would eventually, fall into ruin. Given the presence of a Skull Kid, it is possible this location would be the Lost Woods.
In the end of Ocarina of Time, Navi flew away from Link in the Temple of Time. She flew towards a window ahead of the Pedestal of Time. When Link created the clear staircase, it went toward a window very close to the location Navi flew to. Many believe that Navi went to this "secret area" in the Temple of Time when she left Link.