Garo
Boy Wonder
The Temple of Time and the Sacred Grove have both been the resting places of the Master Sword throughout the series, and now that we have finally seen the creation of the Master Sword, we may be able to finally put to rest some of the bizarre contradictions of these sacred places. This thread will examine plot details - including the ending - of Skyward Sword. If you have not finished Skyward Sword, I would advise you turn back now or else be spoiled.
Let's first examine the facts:
(If there are any inaccuracies in the above table, please point them out to me so that I may fix them! It's been a while since I've played some of these so my memory may be a bit rusty.)
Now there are a few contradictions with the facts as presented to us with the timeline as we understand it. Let's outline the history of the Master Sword so we can identify these places.
The Master Sword's History
In Skyward Sword, the Master Sword starts out as the Goddess Sword, and throughout the course of the game, it becomes the Master Sword through the strengthening of the blade with the three Sacred Flames. At the end of the game, Fi instructs Link to seal the sword - and, consequently, her - into the pedestal within the Sealed Temple (formerly the Temple of Hylia). There it rests. In Skyward Sword, the Master Sword ends the game in the Sealed Temple within Faron Woods, and not within the Temple of Time, which exists in the game within the Lanayru Desert.
In Ocarina of Time, the Master Sword rests in the Pedestal of Time within the Temple of Time. The Temple of Time is not the Sealed Temple, however, as it exists just outside of Castle Town, and not in the forest. Using the Twilight Princess divisions of the three provinces, Castle Town exists within the Lanayru province, making it very plausible that the Temple of Time that was in the desert is the very same Temple of Time outside of Castle Town in Ocarina of Time. Nevertheless, this is the first discontinuity - at some point, the Master Sword was moved from the Sealed Temple to the Temple of Time.
In the adult timeline continuity, Wind Waker comes next, and here the Master Sword - though initially dull - is found inside a secret chamber in Hyrule Castle, and not the Temple of Time. While we never see the Master Sword returned to the Temple of Time in the adult ending of Ocarina of Time, we can assume that this occurred. As such, it is a slight discontinuity that the sword now rests in Hyrule Castle. Given, however, that the forces of Ganon were assaulting Hyrule with no hero to stop them (an assault that appears to still be continuing outside the magical barrier to Hyrule Castle), it is very much possible that the sword was moved to Hyrule Castle for both the safety of the sword as well as sealing some of Ganon's power (it is equally possible that the sword was moved to Hyrule Castle after the events of Ocarina of Time rather than being returned to the Temple of Time, since the Door of Time appeared to be wide open). At the end of the game, the restored sword is driven into Ganon's head, where it rests. It does not appear in the adult timeline again.
In the child timeline, the Master Sword next appears in Twilight Princess, where Link draws it from the pedestal within the Sacred Grove to return to his human form after Zant embedded the Twilight Splinter in his head. Once again, this is a discontinuity - the sword was never drawn from its pedestal in the Temple of Time in the child timeline. However, there is no sign of the Temple of Time in the present day of Twilight Princess - while it appears as a dungeon, it takes place in the distant past. What's more, that dungeon is in the distant past of the Sacred Grove, suggesting that the Sacred Grove (this is the earliest appearance of the Sacred Grove chronologically) is actually the ruins of the Temple of Time. Yet the Temple of Time, up until this point, never existed in the Faron province. We'll come back to this later with a possible explanation - for now, know that this is a discontinuity. The sword is returned to the Sacred Grove at the end of the game.
A Seal War later (it is commonly accepted that the Seal War occurs after Twilight Princess at some point), A Link to the Past occurs. Here, the Master Sword is in the Sacred Grove, which is deep in the Lost Woods - just as it was in Twilight Princess. He draws the sword, whacks Ganon with it, and returns it to the Sacred Grove, where it sleeps forever - the game even says so! No discontinuity here.
So our two major discontinuities occur between Skyward Sword and Ocarina of Time, and then between Ocarina of Time and Twilight Princess. Below, I will explain my theory that reconciles these conflicts to some extent.
Two Temples: The Dual Resting Places of the Master Sword
I'll come right out and say it: I think there are two Temples of Time.
This may seem like utter nonsense, but hear me out. In Skyward Sword, we go into the Temple of Time. This Temple of Time is located in the Lanayru province, just as the one in Ocarina of Time would be. There, Zelda and Impa escape into the Door of Time leading to the distant past, which is then destroyed before Ghirahim can pursue them. Link needs to get to Zelda, so the next portion of his quest becomes finding another Door of Time to make his way into the past. The other Door of Time is located in the Sealed Temple, formerly the Temple of Hylia, deep in the Faron Woods.
Hey wait, that sounds familiar... sort of like the... Sacred Grove?
I am suggesting that the Sealed Temple became another Temple of Time, and that this temple is the one we explore in Twilight Princess, and that the pedestal Link places the sword in becomes the Sacred Grove's pedestal far in the future. The basis for this theory is the presence of the two Doors of Time in the Temple of Time and the Sealed Temple, which (correct me if I am wrong) Impa said are the only two Doors in existence.
Now, how does this fix our discontinuities?
The Temple of Time in Lanayru Desert is the main, more grandiose Temple of Time, as evidenced by the massive Royal Crest in the air above it. This is the Temple that Impa and Zelda defaulted to in their journey to return to the past, rather than the Sealed Temple. The Gate of Time there appeared to have already been operational, unlike the one at the Sealed Temple which required Link to create the Master Sword to activate. All these signs point to the Temple of Time being the dominant of the two, with the Sealed Temple as the sort of backup temple. Thus it would not be too egregious to suggest that the Royal Family moved the sacred blade from its resting place at the Sealed Temple (which would become the Sacred Grove) to the Temple of Time near the newly erected Hyrule Castle and Castle Town. This would reconcile the perceived discontinuity between Ocarina of Time's beginning and Skyward Sword's ending.
As for the latter discontinuity, the existence of two Temples resolves this easily. There is absolutely no evidence of the Temple of Time that existed in Lanayru Desert in the present of Twilight Princess - at some point, the Temple was destroyed most likely for unknown reasons. Thus, the Master Sword was returned to its initial resting place in the Sealed Temple/Sacred Grove. When Link travels back in time to the "Temple of Time", he is in fact exploring the Sealed Temple and not the Temple of Time we all know and love.
With this in mind, our table above looks like this:
And the history of the Master Sword looks like this:
Created (SS) ---> Rests in the Sealed Temple (SS) ---> Moved to the Temple of Time ---> Drawn from the Temple of Time (OoT) --->
Adult: Moved to Hyrule Castle for safety during Ganon's return before the flood ---> Drawn (WW) ---> Kills Ganon (WW)
Child: Moved to Sacred Grove after Temple of Time destroyed ---> Drawn (TP) ---> Returned to Grove (TP) ---> Drawn (ALttP) ---> Returned (ALttP) ---> Rests forever
In summation:
There are two Temples of Time, and two resting places for the Master Sword. Over time, the temples deteriorate, and the Master Sword is moved between them as needed to keep the sacred blade safe and hidden while still protecting Hyrule.
Let's first examine the facts:

(If there are any inaccuracies in the above table, please point them out to me so that I may fix them! It's been a while since I've played some of these so my memory may be a bit rusty.)
Now there are a few contradictions with the facts as presented to us with the timeline as we understand it. Let's outline the history of the Master Sword so we can identify these places.
The Master Sword's History
In Skyward Sword, the Master Sword starts out as the Goddess Sword, and throughout the course of the game, it becomes the Master Sword through the strengthening of the blade with the three Sacred Flames. At the end of the game, Fi instructs Link to seal the sword - and, consequently, her - into the pedestal within the Sealed Temple (formerly the Temple of Hylia). There it rests. In Skyward Sword, the Master Sword ends the game in the Sealed Temple within Faron Woods, and not within the Temple of Time, which exists in the game within the Lanayru Desert.
In Ocarina of Time, the Master Sword rests in the Pedestal of Time within the Temple of Time. The Temple of Time is not the Sealed Temple, however, as it exists just outside of Castle Town, and not in the forest. Using the Twilight Princess divisions of the three provinces, Castle Town exists within the Lanayru province, making it very plausible that the Temple of Time that was in the desert is the very same Temple of Time outside of Castle Town in Ocarina of Time. Nevertheless, this is the first discontinuity - at some point, the Master Sword was moved from the Sealed Temple to the Temple of Time.
In the adult timeline continuity, Wind Waker comes next, and here the Master Sword - though initially dull - is found inside a secret chamber in Hyrule Castle, and not the Temple of Time. While we never see the Master Sword returned to the Temple of Time in the adult ending of Ocarina of Time, we can assume that this occurred. As such, it is a slight discontinuity that the sword now rests in Hyrule Castle. Given, however, that the forces of Ganon were assaulting Hyrule with no hero to stop them (an assault that appears to still be continuing outside the magical barrier to Hyrule Castle), it is very much possible that the sword was moved to Hyrule Castle for both the safety of the sword as well as sealing some of Ganon's power (it is equally possible that the sword was moved to Hyrule Castle after the events of Ocarina of Time rather than being returned to the Temple of Time, since the Door of Time appeared to be wide open). At the end of the game, the restored sword is driven into Ganon's head, where it rests. It does not appear in the adult timeline again.
In the child timeline, the Master Sword next appears in Twilight Princess, where Link draws it from the pedestal within the Sacred Grove to return to his human form after Zant embedded the Twilight Splinter in his head. Once again, this is a discontinuity - the sword was never drawn from its pedestal in the Temple of Time in the child timeline. However, there is no sign of the Temple of Time in the present day of Twilight Princess - while it appears as a dungeon, it takes place in the distant past. What's more, that dungeon is in the distant past of the Sacred Grove, suggesting that the Sacred Grove (this is the earliest appearance of the Sacred Grove chronologically) is actually the ruins of the Temple of Time. Yet the Temple of Time, up until this point, never existed in the Faron province. We'll come back to this later with a possible explanation - for now, know that this is a discontinuity. The sword is returned to the Sacred Grove at the end of the game.
A Seal War later (it is commonly accepted that the Seal War occurs after Twilight Princess at some point), A Link to the Past occurs. Here, the Master Sword is in the Sacred Grove, which is deep in the Lost Woods - just as it was in Twilight Princess. He draws the sword, whacks Ganon with it, and returns it to the Sacred Grove, where it sleeps forever - the game even says so! No discontinuity here.
So our two major discontinuities occur between Skyward Sword and Ocarina of Time, and then between Ocarina of Time and Twilight Princess. Below, I will explain my theory that reconciles these conflicts to some extent.
Two Temples: The Dual Resting Places of the Master Sword
I'll come right out and say it: I think there are two Temples of Time.
This may seem like utter nonsense, but hear me out. In Skyward Sword, we go into the Temple of Time. This Temple of Time is located in the Lanayru province, just as the one in Ocarina of Time would be. There, Zelda and Impa escape into the Door of Time leading to the distant past, which is then destroyed before Ghirahim can pursue them. Link needs to get to Zelda, so the next portion of his quest becomes finding another Door of Time to make his way into the past. The other Door of Time is located in the Sealed Temple, formerly the Temple of Hylia, deep in the Faron Woods.
Hey wait, that sounds familiar... sort of like the... Sacred Grove?
I am suggesting that the Sealed Temple became another Temple of Time, and that this temple is the one we explore in Twilight Princess, and that the pedestal Link places the sword in becomes the Sacred Grove's pedestal far in the future. The basis for this theory is the presence of the two Doors of Time in the Temple of Time and the Sealed Temple, which (correct me if I am wrong) Impa said are the only two Doors in existence.
Now, how does this fix our discontinuities?
The Temple of Time in Lanayru Desert is the main, more grandiose Temple of Time, as evidenced by the massive Royal Crest in the air above it. This is the Temple that Impa and Zelda defaulted to in their journey to return to the past, rather than the Sealed Temple. The Gate of Time there appeared to have already been operational, unlike the one at the Sealed Temple which required Link to create the Master Sword to activate. All these signs point to the Temple of Time being the dominant of the two, with the Sealed Temple as the sort of backup temple. Thus it would not be too egregious to suggest that the Royal Family moved the sacred blade from its resting place at the Sealed Temple (which would become the Sacred Grove) to the Temple of Time near the newly erected Hyrule Castle and Castle Town. This would reconcile the perceived discontinuity between Ocarina of Time's beginning and Skyward Sword's ending.
As for the latter discontinuity, the existence of two Temples resolves this easily. There is absolutely no evidence of the Temple of Time that existed in Lanayru Desert in the present of Twilight Princess - at some point, the Temple was destroyed most likely for unknown reasons. Thus, the Master Sword was returned to its initial resting place in the Sealed Temple/Sacred Grove. When Link travels back in time to the "Temple of Time", he is in fact exploring the Sealed Temple and not the Temple of Time we all know and love.
With this in mind, our table above looks like this:

And the history of the Master Sword looks like this:
Created (SS) ---> Rests in the Sealed Temple (SS) ---> Moved to the Temple of Time ---> Drawn from the Temple of Time (OoT) --->
Adult: Moved to Hyrule Castle for safety during Ganon's return before the flood ---> Drawn (WW) ---> Kills Ganon (WW)
Child: Moved to Sacred Grove after Temple of Time destroyed ---> Drawn (TP) ---> Returned to Grove (TP) ---> Drawn (ALttP) ---> Returned (ALttP) ---> Rests forever
In summation:
There are two Temples of Time, and two resting places for the Master Sword. Over time, the temples deteriorate, and the Master Sword is moved between them as needed to keep the sacred blade safe and hidden while still protecting Hyrule.
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