The Master sword is the pinnacle of all Zelda weapons, it is often omitted from more minor Zelda games, but is usually the strongest weapon available in all those it appears in.
It normally appears after you have gone through the first set of dungeons (Usually 3), no other weapon is like it and if you pay careful attention you will notimce that it will do more heart damage to regular creatures than your previous sword.
In most places it is found in the sacred realm or the area that was built upon it (Temple of Time in Ocarina of Time) or the most recent exception, the sacred grove in Twilight Princess, However, the grove was confirmed to be a decaying Temple of Time.
The Sword is of Majora Plot significance, its only minor role being in Twilight Princess where, like Zelda herself, it seemed forced in.
 Skyward Sword
The Master Sword's life began as a short blade called the Goddess Sword. This stayed in the sacred temple on the outskirts of Skyloft until Link pulled it from it's pedastal as he was following the weapon's spirit known as Fi. Link used this version of the sword until he was told by the Sealed Grounds' elder to find the 3 sacred flames to empower the weapon. As Link found the 3 sacred flames, the Goddess Sword turned into the Master Sword, but it was not until Princess Zelda awakened from her slumber and used her newfound powers to give the weapon it's legendary power to smite evil from the land. Link used this weapon to eliminate the evil demon Demise in his past form and sealed his spirit into the blade which in several thousand years eliminated Demise completely.
After the events of Skyward Sword, the country of Hyrule was founded by the former inhabitants of Skyloft. The Sage Rauru took the weapon and made it into as of a final key to the place of the Triforce: The Sacred Realm to ensure the Triforce's safe keeping, the weapon itself would also be placed by a sacred magic so that only one with a pure, righteous heart can grip the hilt of the weapon, a building was also erected to ensure the weapon's and the Triforce's safety. That building would known as the Temple of Time. The sword would rest in the Temple of Time for many years.
 Ocarina of Time
Many years have passed since the Master Sword was used, and it is about to be called into action again as an evil man from the Gerudo Dessert named Ganondorf will come to attempt to obtain the Triforce in hopes to conquer Hyrule. A young boy from Kokiri Forest named Link embarks on an adventure to save Hyrule, as he meets the Princess of Hyrule named Zelda, she tells him of her dream and the story of the Triforce, and a way to open the Door of Time (where the Master Sword rests behind). Link must find 3 Spiritual Stones and must have the "Ocarina of Time" and play the "Song of Time" and pull the Master Sword from it's pedestal to open the way to the Sacred Realm. After Link gathers the 3 Spiritual Stones and his encounter with Ganondorf at the walls of Hyrule Castle, he obtains the Ocarina of Time (which Zelda threw into the moat while fleeing from the castle) he ventures to the Temple of Time where he placed the Spiritual Stones at the Alter and used the Ocarina to play the Song of Time, the door opened and he slowly approached the Master Sword and pulled it from it's pedestal. But what Link did not know is that though he had a pure heart but he had yet to realize his destiny of a hero, because of this Link was whisked away to the Sacred Realm which was left open for Ganondorf to obtain the Triforce. Seven years have passed and Link was discovered by Rauru who told him what had happened to Hyrule during Link's 7-year suspension in the sacred Realm. Link understands that he must liberate Hyrule from Ganondorf with the sacred Master Sword.
 A Link to the past
The Master Sword was put to rest by Princess Zelda shortly after the Imprisoning War (if Link were to fall at the hands of Ganondorf). Many years have passed and Hyrule changed dramatically. It would not be until another young boy named Link that would venture throughout Hyrule on a mission by the Hyrulian Princess named Zelda to defeat the evil wizard Agahnim. The only weapon powerful enough to defeat the wizard and his magic is the sacred Master Sword. Link had to travel far and wide and defeat powerful monsters to obtain the 3 Pendants of Virtue which are the keys to retrieve the weapon from the Lost Woods. But as Link pulled the Master Sword from it's pedestal, he hears a distress telepathy message from Zelda saying that Agahnim's forces have found her and are heading to the Sanctuary, once Link got to the Sanctuary they have already taken Zelda and left the sage fatally wounded, but before the sage died, he told Link that Zelda was taken back to Hyrule Castle as a sacrifice to Agahnim so he can break the Sages' seal which separates Hyrule from the Sacred Realm (now known as the Dark World). Link used the Master Sword to defeat Agahnim, but as Link defeats the wizard he uses his magic to bring Link to the Dark World. Link oon realizes that he must rescue the 7 maidens in order to stop Agahnim from conquering Hyrule. During his adventure, Link uses the Master Sword to fight the Dark World's horde of monsters. He also allowed Hyrulain smitheries and Great Fairy magic to make the weapon even stronger. In the end the Master Sword aided Link in his defeat of Agahnim and eventually Ganon and recover the Triforce to not only give Hyrule but the Sacred Realm peace. Link returns the Master Sword to it's pedestal soon after he completes his adventure.
 Twilight Princess
If Link is successful in his fight against Ganondorf, the 7 Sages would cast their seal and send Ganondorf into the sacred Realm. As Link and Zelda stand at the ruins of Ganon's Castle, Zelda tells Link that he must return the Master Sword to the Temple of Time in order to ensure that Ganondorf may never escape from his confinements in the Sacred Realm, by using the Ocarina of Time, Zelda sends Link back to the Temple of Time where Link returns the Master Sword to it's pedestal. Many years have passed since the events. Now, Hyrule is being threatened by a force from an entire world entirely called the Twilight Realm. A farm boy named Link was sent on an adventure by 2 princesses named Zelda and Midna. After liberating Hyrule from the effects of the Twilight Realm and saving Midna from death, Link heads to the deep part of the Faron Woods where he discovers a place of ruins, after completing a trial by 2 statues, he comes across the Master Sword (which also releases Link from his beast form bestowed upon him by the Twilight King Zant. Link uses the weapon to help Midna find the shards of the Twilight Mirror which is the pathway into the Twilight Realm. As Link obtains all of the pieces of the Twilight Mirror and Midna assembles them. they head into the Twilight Realm, and as Link obtains 2 special light objects called Sols, he hits them with his Master Sword which give the weapon the power to smite the Twilight, with this new power, Link used the weapon to defeat both Zant and eventually Ganondorf. Though the fate of the weapon is unknown after Link's fight with Ganondorf.
 The Wind Waker
If Link is successful in his fight against Ganondorf, the 7 Sages would cast their seal and send Ganondorf into the sacred Realm. As Link and Zelda stand at the ruins of Ganon's Castle, Zelda tells Link that he must return the Master Sword to the Temple of Time in order to ensure that Ganondorf may never escape from his confinements in the Sacred Realm, by using the Ocarina of Time, Zelda sends Link back to the Temple of Time where Link returns the Master Sword to it's pedestal. Many years have passed since the events, and Ganondorf is about to escape from the confinements of the Sacred Realm and once again wreak havoc on Hyrule. Because link was a part of another era in Hyrule, he was unable to help the people in this era, who had no choice but to appeal to the goddesses of Hyrule. Eventually, the King of Hyrule had entrusted his land to the Goddesses who advise the survivors to flee to the mountains and used magical water to flood the land and seal Hyrule and Ganondorf. Several years have passed since the flooding of Hyrule, a young boy named Link who lived on Outset Island embarked on an adventure to rescue his sister Aryll who have been taken away by a giant bird. Aided by a band of pirates led by a woman named Tetra he ventures out to the Great Sea. What he unlocks is called the Tower of the Gods, after passing the tower's trials, Link was led into the flooded Hyrule and he ventures into the castle, after connecting 3 triangular blocks (resembling the Triforce), he was brought into an underground area where he finds the master sword replica. Possibly due to the flooding of Hyrule, the Master Sword was separated from it's abilities to smite evil, Link must restore the weapon's powers if he is to eliminate Ganondorf. With the help from other beings of the great sea (Medli and Makar who are descendants of other sages of the former Hyrule) Link restored the power to the Master Sword. Link goes on to fight Ganondorf who was about to obtain the true force of the Triforce until the King of Hyrule stopped him, and with the help of Tetra (who was Princess Zelda re-incarnated) Link defeated Ganondorf with the Master Sword as the evil King turned into stone. The Master Sword is still stuck in Ganondorf's remains as Hyrule was re-flooded.
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