The Forest Temple becomes the resting place for the Master Sword.

In Ocarina of Time, the Forest Temple is located at the deepest, furthest, darkest end of the Lost Woods. Once you reach it, you cannot initially enter; its narrow staircase has been destroyed. In A Link To The Past and Twilight Princess, you acquire the Master Sword after many trials in the deepest reaches of those same woods — first, it seems, in Twilight Princess, where some of the structures remain, and then in A Link To The Past, where almost everything but the pedestal has been destroyed or too overgrown to discern from foliage.

There's more to this, though. Notice the architecture of the Forest Temple. The first thing we discover is that it's got a narrow stairway. That sort of thing isn't characteristic of lavish palaces or other places of residence — we're dealing with a battle fortress designed and used in warfare. And the more we look at the Forest Temple, the more evidence we find that it both both built and used with violent intent. If the fact that it has battlements wasn't enough, it also tends towards narrow hallways. Its characteristic item is the bow — perfect for defending a superior position.

It's also haunted by four ghosts who must be destroyed before the inner sanctum can be reached, and I suspect this inner sanctum is ultimately what becomes the resting place for the Master Sword. But there are a lot of questions left unanswered.

Were the ghosts put there by purpose? Was it Ganondorf who wrought them, or the ancient Hylians who defended the fortress? Or are the ghosts chained to the temple by other means? Punishment for treachery? The fortress obviously fell, after all, and become home to all manner of vile monsters. How could such a well-defended fortress fall while Hylians yet stood to defend it otherwise?

My theory is this:

The Forest Temple is a Hylian fortress sanctuary built in the furthest reaches of the Lost Woods for both secrecy and safety. Any incoming enemy would have to brave the dark magicks of the forest, make their way through the courtyard maze and then assault up narrow stairs and through narrow hallways. Any advancing force would be falling into a deathtrap, especially fighting against the highly adept Hylians.

Lust for power and riches corrupted the hearts of four Hylian sorcerers, who sabotaged the defenses and let the enemy hordes in. As punishment for their treachery, what remained of the other Hylian mages cursed them to stalk the halls of the fortress until defeated in battle by a hero pure of heart.

Ultimately, the inner sanctum was never breached, which is why it appears untouched during Ocarina of Time.

After the events of Ocarina of Time and Wind Waker, the Sages decide to keep the Master Sword in the inner sanctum for both safety and as a monument to Hylian prowess in battle, as was reborn in Link. From then on, the young heroes who sought the power of evil's bane had to make a pilgrimage to the site of the Hylians most gruesome massacre, walking where blood was once spilled as a symbol of their will to right the ills of Hyrule.

sounds reasonable, very reasonable.

And as an added bonus, it would scare the shit out of any not-pure-hearted treasure seekers.