In Twilight Princess, I would put the Great Deku Tree in a new zone that you access from Lake Hylia, but after you've entered Sacred Grove. I would put some roots of the Great Deku Tree over the final exit of Sacred Grove before the Temple of Time. And we must find where the roots are coming from. The investigation leads us a shrouded area connected to Lake Hylia, where the Great Deku Tree resides. The Great Deku Tree would be corrupted by Shadows and we must remove the parasites that are growing on the tree. Afterwards, the Great Deku Tree would thank us and open a shortcut back to the Sacred Grove where the roots have been removed.

In the new area containing the Deku Tree would be some architecture resembling the Forest Temple and also the Temple of Time, that suggests the three areas were once connected. As well as a very damaged mural that vaguely shows the adventures of the Hero of Time.…