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Mystery Honeycombs are a variey of Honeycombs found exclusively in Banjo-Tooie. They are identifiable from regular Honeycombs as they have question marks (?) on them.

Mystery Honeycombs are like sophisticated Skill Honeycombs, as they will cycle through the Honeycomb Bar at random. The player must be very careful as to not stop the bar at low level, or they may end up walking away with less energy than they initially had. While the cycle is slow and easy to stop in earlier levels, the speed will increase in the later levels.