Mystery Seed
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You will first obtain the Mystery Seed in Oracle of Ages while you're sent on a hunt to find Mystery Seeds for Queen Ambi. The seeds are located at Deku Forest, once you find them they will take you back to Queen Ambi's Palace, there she will reward you with Bombs. After all of this you're free to go back and get more Mystery Seeds.
You will first obtain the Mystery Seed in Oracle of Seasons after you go to Subrosia and receive the Rod of Seasons along with the Power of Winter. After you come back from Subrosia you will be able to freeze the water by changing the season to winter. Once you walk over it and go through the forest a bit you'll eventually come up to a Mystery Seed tree and an Owl Statue.