Tree Stumps & Disk #22
The base of some tree stumps on Kyoto feature a hole shaped like an arrow. Additionally, breaking certain trees will occasionally reveal a floppy disk marked "#22" only visible to some players. This is a reference to the "stump joke" from the floppy disk version of The Secret of Monkey Island, in which Guybrush Threepwood peers down a hole in a tree stump at a system of catacombs below. He attempts to squeeze through, and the game prompts the player in "insert Disk #22", "Disk #36", and "Disk #114" to advance. These disks do not physically exist, and so upon the player's failure to insert them, Guybrush says he'll have to skip that part of the game.
This was seemingly first teased in the credits scroll of Season 3:
"...ok to all of you EE hunters out there... missing discs..."
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Disk #22 after appearing from a tree breaking
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Close up of Disk #22
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A type of tree that triggers disks
New Zealand Fantail
Graffiti of a New Zealand Fantail bird can be found across Kyoto. During development of Kyoto, Embark Studios level designer Midas got engaged in New Zealand and took particular interest in the bird.