The general assumption is that the Twilight Princess Forest Temple is the remains of the Deku Tree because it's in the exact right place and has the Kokiri symbol on its doors, just like the Deku Tree's interior did. The Forest Temple of Ocarina of Time is thought to have fallen in over that century, but some believe it to be the ruins the Skull Kid battles Link inside of in Twilight Princess. This is somewhat supported by the fact that the middle of the arena has a square-like brown floor, looking much like the top of the Forest Temple's elevator melded with the floor as it was in Ocarina of Time. This is disputed by its close proximity to the Temple of Time's ruins though, making some believe it may have been the ruins of the old Hyrule Castle Town. However, the doorway the Skull Kid opened could have been a portal to another part of Hyrule, where the Temple of Time stood. But as for the Forest Temple of Twilight Princess, it's strongly supported that it was the remains of the Deku Tree.
It's obvious from the Kokiri symbol within the Forest Temple that the Kokiri had onced lived in that region, but like the Kokiri, the Deku Tree Sprout likely vanished along with their civilization (a large part of the ground in front of the Forest Temple had eroded away, likely washing away the Deku Tree Sprout's body). However, it appears that there are two trees to the Forest Temple, and it could be that the front one is the Deku Tree Sprout while the back one is the dead remains of the Great Deku Tree. It appears that the forest's spirits had largely vanished over that century as the humans and Hylians established their Ordona Province and tamed the forest. So the Kokiri and the Deku Tree Sprout likely vanished during that period, as the forest was tamed by humans, somewhat like Narnia's forest spirits sank into obscurity when the Telmarines invaded Narnia and tamed the forests. If you look closely, Ordona Village looks remarkably similar to the Kokiri settlement, and it's assumed they are the same place due to its close proximity to the Forest Temple.
It had to of grown into something like a Deku Tree while it was there... maybe the Kokiri evolved into humans because of the Deku Sprout evolved into a spirit... It's too bad MM was inbetween OoT and TP, we know nothing about it...
That is why I said the front tree is likely the Deku Tree Sprout, devoid of its spirit since the forest had changed during that century. The back tree is likely the Deku Tree, and if you look at the back tree, its bark is notably darker and looks older than the entrace tree. This further supports the two trees being the Great Deku Tree and the Deku Tree Sprout. The Kokiri may have hidden deeper in the forest once humans took over their forest, like the Skull Kid. Without the Deku Tree's protection, they likely passed away or went into hiding deep within the forest's inner sanctums. They had obviously once been in that region though, as evidenced by their symbol.
The smaller tree is the back one (I think... we really need an image, though), so that means the deku tree rotted... Now I wish LoZ games were longer and more elaborate... OoT was so good 'cuz everything was based on it...
That would make sense, since dead trees usually deteriorate over time due the elements. Yes, Ocarina of Time is so beloved by fans because that's where the series' continuity gets started, and we see the introduction of the major characters there. Not to mention it covers the Imprisoning War, one of the most exciting and most famous wars in all the series.
 Some things can be explained away but this is word for word OniDark Link 22:25, July 19, 2010 (UTC)
Oni, you are the new guy in charge of making sure they don't steal any more of our stuff.
Isn't Master quest simply a hard mode for ocarina of time? How is it Non-Canon? 09MurphyM (talk)
Because the actual version is canon. --EveryDayJoe45 (talk) 00:36, September 14, 2010 (UTC)
About the odd chanting and the flute that accompanies it...
It turns out that chanting was a sample named "African 098-B". For years, playing the game when I was younger, I thought that was Link's voice making those noises. Shows how much I knew back then.Whirl Roller (talk) 13:49, June 8, 2014 (UTC)