The Great Beings tampered with the makeup of the Blade Burrowers, which causes the Rahi to begin digging a series of tunnels as a result. The Blade Burrowers form was created by Makuta Mutran, and used by Barraki Kalmah during his reign in the League of Six Kingdoms. Mutran programmed the Blade Burrowers he sent to die after a span of three days.
While searching through the remains of Kalmah's fortress after the League's defeat, Mutran noticed the Burrowers, who had survived their expiration date. He was intrigued by the series of tunnels they were creating, though he was unable to decipher the meaning. He later had a captured Toa with a Kanohi Rau attempt to contact the Rahi, but the Rahi were unable to convey the meaning behind their behavior.
The map that the Blade Burrowers make is the symbol that represents the Three Virtues. It is meant to remind Mata Nui of his mission.
Anyway, given the gathered information above, I will point out that Mutran did not design the burrowers to create their tunnel pattern (since it was a mystery to him), and that he specifically designed these specific Rahi to die after three days. The quote above specifically says that the Great Beings tampered with the burrowers (probably to extend their lifespan and to make them build the pattern).
Now, where are the Great Beings during that time frame? They were present during the robot's creation, but I don't see them exactly running about 15,000 to 20,000 years after (BS01 says that the League was defeated "80,000 years ago"). Somebody modified those burrowers, and it would have to have been under Kalmah's nose, or between Mutran and Kalmah, seeing as either didn't know what the map was or why it was in the burrower's brains. Likely either party, or the beings they used to transport the burrowers, would have noticed if a Great Being showed up in all his glory (Hey, let me modify these!). And once the mystery was brought up, I imagine Kalmah the Warlord would have interrogated the beings involved in holding and/or shipping the Rahi, and it would have came out.
But the Hidden GB would have brought little or no attention. He might have simply been involved in the transport operation to begin with and could bluff his way out. Also, this particular individual, with his penchant for observation, would likely have wanted to observe the League for information, which could have placed him in this position (important enough to observe, but not really be noticed). A person involved in transportation would know what is going to whom, and possibly have access to port gossip in Kalmah's fortress. But Kalmah and Mutran would likely view such an individual as just another minion, which would likely go unnoticed.
So go ahead and point out all the holes the size of blade burrower's tunnels in my theory.
Edited by fishers64, Feb 05 2012 - 10:22 PM.