DeepTower isn't a tower at all, but a massive tree and is, in fact, analogous to the World Tree.The lower levels at least have branches and at the very top of the NightWalk side of the tower where you meet the "find the flowers" ghost, there is a green roof, which could suggest a large canopy higher up. It might not be something that would strike players' minds initially, but taking a look at a full map of the game (Warning: spoilers, obviously; also, large image size)◊, it becomes pretty obvious. However, the WMG doesn't end there: when you explore the area where the roots might be, you find yourself in BlancLand, where the level design takes on a minimalistic quality. My guess here is that at the "roots" of the world, things were created to be at its most basic and as the tree grew and developed, the world began grow as well and become more complex.
Shakespeare the Ninja wrote the diary page in the secret library.It talks of learning from the spirits and using the energy inside them. He has teleportation powers and seems to glow with energy...
Shakespeare the Ninja is a transformed bird. He can apparently fly, and he knows about both birds and the ghosts...
The game takes place on the edge of a large floating continent.CloudRun, MountSide, BlackCastle and the Bottom aren't at the very bottom per se. They are very high on Earth and the said floating continent is even higher.note
The endboss is an Eldritch Abomination.The final boss couldn't possibly qualify as anything else. The humanoid first form at least makes some sense, but after that the game cranks up the Mind Screw dial by having he/she/it take the form of two separate energy balls, then a walking turret thing, then making the turret's head inexplicably float and finishing up with a giant pair of eyes in the background; each transformation is preceded with the sparkly, faded-purple essence of the first form flying off the screen, not actually transforming or reforming itself. The vaguest explanation I can offer for this is that the final boss is an Energy Being and that the giant grey cloud in the background is actually his/her/its "body" and it is trying to kill the player character with attacks and corporeal entities formed out of its own Soul Power.