There is a locked room in the Toilet Dungeon, in Chapter 8, which has water leaking from under its door. It is never accessible during normal gameplay, and the door is non-functional, but if you use a walk through walls code in the next room, you can actually access the flooded room. There are no NPCs inside, and no solidity is programmed.
There is also a room in another corridor that is rendered inaccessible when a man rushes in and prevents you from entering. Walking through the walls here reveals that it is filled with toilet paper.
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In the game files, there lies two strange graphics of Duster and Kumatora in unused clothing. They appear to be teleporting, but it's very different from the PSI Teleport used in the Mother trilogy and is most likely unrelated. What the graphics could have been used for is anyone's guess.
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A low quality picture of the Ostrich Burgers Historic Summit Inn Cafe on Route 66. It's possible that it was simply inserted into the game to test how the game displayed graphics.
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More info at:
http://tcrf.net/Mother_3