Farore’s Pearl is the second of the pearls that is obtained by Link in The Wind Waker, being kept by the Great Deku Tree in the Forest Haven. It is initially going to be given to Link after the Korok’s annual ceremony, until Linder flies in, crying that Makar had fallen into the Forbidden Forest. After Link rescues Makar, the Great Deku Tree bestows Farore’s Pearl upon the young hero. Link later on places the pearl on Eastern Triangle Island to raise the Tower of the Gods out of the Great Sea.
Farore’s Pearl has the same mark on it as the symbol for the Tune of Echoes from Oracle of Ages and as the Courage Gems from Phantom Hourglass. The same symbol also appears on a door inside the Temple of the Ocean King. Link must complete the symbol in Skyward Sword by using his Skyward Strike’s drawing powers. – Zelda Wiki