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The Clocktower on Myst Island served as the key to unlock one of the island's "places of protection", a series of puzzle-protected storage facilities for the various Ages that Atrus had written while he and his family lived there. This key protected the Linking Book to the Mechanical Age. It rests just offshore on the southern end of the island, and can be reached by a path of gears which rise from the water when the clocktower is set to the proper time.
Within the tower, a combination lock made of 3 horizontal gears is used to open the giant gears on the island's north side. The lock is operated by pulling the levers on either side of the gear assembly. The left lever advances the top two gears, and the right lever advances the bottom two. Holding a lever down will advance the center gear on its own. The lock uses a counterweight to drive the movement of the gears, so the puzzle must be solved within a certain number of movements. Once the correct combination is set, the Mechanical Age's place of protection opens, as indicated by the small model gear set in front of the lock.