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The Moon's Tear symbolizes Isis's tears, and the later flood. You get the tear after you do the cave of the nymphs sequence, and look through the telescope(become a being of light). Majora's Mask ends with a rainbow. God used the rainbow to mark his promise that he would never flood the world again. Here they allude to the flood with Isis's tear, show you the rainbow at the end, and the next game released was Wind Waker. The Wind Waker was entirely flooded. 

It's  a satanic inversion of the story. They are making god into a liar who floods the humans after the rainbow.

https://youtube.com/watch?v=F1IqUwpint4
21:23 rainbow emerges after Termina is saved

Ocarina of Time had a rainbow bridge that took you up to Gannon's castle. More satanic rainbow symbolism.
https://zelda.gamepedia.com/Rainbow_Bridge

https://zelda.gamepedia.com/Moon%27s_Tear
Moon's Tears are fall from the surface of the Moon to Termina, so named by Professor Shikashi because they fall from what appears to be the Moon's eye.[1] They're rumored to be the shiniest stones in the world and are consequently highly valuable.[2]

Professor Shikashi keeps one of these rare stones in a display case, which the Skull Kid threatened to steal.[3] Link can acquire a single Moon's Tear for himself by peering through the telescope in the Astral Observatory. When Link takes a closer look at the Skull Kid,[4] who is fooling around on the top of the Clock Tower,[5] a Tear will fall from the Moon and impact just outside the observatory with a bang. Afterwards, the Skull Kid will taunt Link and disappear. The young hero can then find it embedded in a small crater where it landed, just within the fenced area outside the Observatory door.

kikepedia/wiki/Isis
Sirius's heliacal rising, just before the start of the Nile flood, gave Sopdet a close connection with the flood and the resulting growth of plants.[61] 
> Partly because of her relationship with Sopdet, Isis was also linked with the flood,[62] which was sometimes equated with the tears she shed for Osiris.

By Ptolemaic times she was connected with rain, which Egyptian texts call a "Nile in the sky"; with the sun as the protector of Ra's barque;[64] and with the moon, possibly because she was linked with the Greek lunar goddess Artemis by a shared connection with an Egyptian fertility goddess, Bastet.[65] In hymns inscribed at Philae she is called the "Lady of Heaven" whose dominion over the sky parallels Osiris's rule over the Duat and Horus's kingship on earth.

> Isis was often characterized as a moon goddess, paralleling the solar characteristics of Serapis.
She was also seen as a cosmic goddess more generally. Various texts claim she organized the behavior of the sun, moon, and stars, governing time and the seasons which, in turn, guaranteed the fertility of the earth.[160] These texts also credit her with inventing agriculture, establishing laws, and devising or promoting other elements of human society. This idea derives from older Greek traditions about the role of various Greek deities and culture heroes, including Demeter, in establishing civilization.