Spoiler What Happens to the Master Sword in the Adult Timeline?

[Blue Window]

To Zora_Waterfall

Zelda is confirmed to be the leader of the Sages in OoT.

And the other, who holds the Triforce of Wisdom... is the seventh Sage, who is destined to be the leader of them all... It is I, the Princess of Hyrule, Zelda.

About the Master Sword

The reason why there is one Master Sword on the AT and on the CT is because the CT MS is the one that always have been there. It's not harder than that.

AT: Link talks with Zelda---Link goes to the ToT---Link takes the MS --- Adventure --- Link talks with Zelda --- The MS remains on the AT
CT: Link talks with Zelda---Link goes to the ToT---(!)Link does not take the MS(/puts it back)---MM

(!) is where Link ends up on the CT (could be earlier, though).

/Blue Window

 

[Bétùm]

I think the real problem here is that Time is literally not meant to be fully understood by the human brain.

The timeline spilt occurs in two "places", in a way. A) Zelda sends Link back to before he ever pulled the MS at all. We catch YLink about to hurtle through time for his first time, when he (with his newfound adult memories), stops himself and hops down from the pedestal.
In the AT, we can only assume that the MS is left in the same place as all of Link's other equipment that disappears when he reverts to his youthful form.

 

[Fierce_Deity]

During the ending of OoT, Zelda plays a tune. Link is then seen floating upward before the camera pans away. Next Link is in a transport beam NOT touching the Master Sword but rather staring at it. However, when you are playing and you place the MS into the pedestal and entire different effect is seen. Also when you appear as a child, Links hops down from the pedestal (he doesn't at the ending)This is not speculation, it is what happens in the game. See youtube video if you need proof.


Now for speculation based on those events. When Zelda is sending Link back, I strongly believe the Master Sword is left behind right there where you battled Ganon. Hyrule Castle is destroyed so a new one is eventually built around the Master Sword. In Wind Waker the Master Sword is not in the Temple of Time but underneath Hyrule Castle.

After Link is returned to his child form, he never removes the MS, it remains in the Temple of Time until Twilight Princess.

 

[Links Ocarina 7]

Link puts it back and Zelda sends him back in time I belive

 

[Fierce_Deity]

no Link puts it back and Zelda sends him back in time.

When is this shown in the game? If it is put back in the Temple of Time, explain then how it gets from The Temple of Time to beneath Hyrule Castle in Wind Waker as only the Chosen One can wield it. You can't just pop up and say "no" without explanation.

 

[MissingLink]

We can't assume everything from the lack of detail showed in the cutscenes. Link put the sword back before turning into a kid (that was the only way). This is why it is there when he awakens as his young self.

 

[guapo2003]

I believe the Master Sword is still in the Temple of Time. When Link went was transferred back as a kid, he put the Master Sword back into he pedestal therefore, the door to it was shut again, and can only be opened with the Ocarina of Time, so when he went back to tell Zelda about everything that's going to happen, she gave him her Ocaina and he went away so Ganondorf could not get access to The Temple of Time.

 

[Blue Window]

The only moment in time where the Master Sword could have left Link was between Zelda sent him away in a blue light on the AT and him leaving that timeline. Ergo, there are two possibilities to what could have happened:
1) Link left the sword himself.
2) The sword remained for some other reason.

Since Zelda wants Link to put back the Master Sword he must have done that on the AT. We know this because the Master Sword was never drawn on the CT (thanks to Hyrule Historia!). Thus, the most plausible explanation is that Zelda sent Link to the Temple of Time, where he put the Sword back and was sent back in time, but that Zelda's magic made him go to the CT and to a time before he originally met Zelda.

/Blue Window