To get the moon's tear you must go through the bomber's secret passage or turn into Deku link and fly over the gate to the observatory using the Deku flower.
Then climb the stairs to the top of the observatory, and talk to the old guy. He will ask you if you want to look through that space scope thingy. Say "YES" and zoom in on thetop of the clock tower.
A small scene thing should start with the Skull Kid. The thing that falls from the moon is the moon's tear.
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