The owl had told Link to fly like a bird, but Link had never heard of anything that could allow him to soar above the clouds. He remembered a statue in Mabe Village, on which was inscribed the brief epitaph "Here Sleeps the Flying Rooster," but Link didn't know how a dead bird could help him.

While searching around Ukuku Prairie, Link entered the Signpost Maze. A signpost told him to go south, so he walked south until he reached another signpost. This one told him to go a different direction. Link walked through the maze, trying not to lose track of where the last sign had told him to go. The last sign told Link that he had done a great job, and a secret passage opened up.

Walking down into the underground cave, Link found a huge frog (who looked like a certain Wart from another game) and two smaller ones. The big frog introduced himself as Mamu, and explained that he was a famous singer on tour. For 300 Rupees he offered to sing a previously unreleased cut for Link. Link was really starting to like music, and he thought maybe he could learn the song on his Ocarina, so he payed the Rupees and listened to the frogs jam. The lights dimmed and spotlights shown on the three frogs. A wild dance ensued, punctuated by the croaking vocals of Mamu. At the end of the performance Mamu thanked the one member of his audience, Link. Link secretly thanked Mamu, because now he had learned the Frog's Song of Soul, a very moving tune which could even liven up unliving things.

Back in Mabe Village, Link pushed the rooster statue to reveal an underground crypt, the resting place of the Flying Rooster. All that was left of the rooster was a skeleton, but Link played the Frog's Song of Soul. The rooster's spirit appeared, flew around, and, entering the bones of the rooster, made the Flying Rooster come back to life! The rooster was very friendly and followed Link around wherever he went.

Link began to explore the Tal Tal Mountain Range, and before he had gone far the owl appeared and told him that his path was not easy, but he was almost there. Instructing him to go east, he told Link that the Wind Fish was growing restless, and flew off. Link reached a Hen House, and the owner told him that he had been trying to make his chickens fly. Then he noticed with amazement that Link's rooster was actually flying, and he suggested that Link hold the rooster over his head so he could fly too.

Link put this advice to good use deep inside a cave in the Tal Tal Mountains. He found himself staring down into a vast, wide pit, which could only be traversed by one who could fly. Link picked up the rooster and held him over his head, and the rooster flew up, taking Link with him. Using the rooster to fly over the pit, Link was able to get the Bird Key. Another cave led Link to a face statue, which warned him that he should beware the bird that lived in the Eagle's Tower. The Eagle's Tower was on the mountain's summit, and when Link put the Bird Key into the Bird Keyhole, the entire tower rotated so that the entrance faced Link instead of facing the sheer drop on the other side. Leaving the rooster outside, Link entered the Eagle's Tower.

While he was exploring, Link noticed that several pillars were holding up a higher floor. An owl statue told him that the riddle would be solved when the pillars fell, but Link didn't know how he could destroy the pillars. He finally figured out that if picked up the crystal ball that was lying around in one room, he could throw it at the pillars to make them crumble to the ground. He destroyed two pillars without any problems, but the two other pillars would take some work to get to.

Some eyeball guards had been shooting magical beams at Link, which was irritating because he couldn't block them with his shield. He had to either dodge the beams or run past when the rotating eyeball wasn't looking his way. On the second floor of the Eagle's Tower Link found the Mirror Shield, which could turn back the beams Link couldn't block before! Link destroyed the third pillar, and later found himself in the same room with a Hinox. Two braziers shot fire at Link, and Link had to jump around to avoid falling in pits. The Hinox threw bombs and tried to charge Link, but Link shot arrows at the cyclops until he was destroyed.

Link gave over trying to destroy the fourth pillar for a while and climbed to the third floor. He saw narrow walkways which led over deep pits, and saw from his map that there was no way to reach the top floor other than going over the pits. Confused, Link left that until later. He had something else to worry about, specifically a monster with a bad attitude, the Grim Creeper. Challenging Link, he called in his thugs, waves of flying creatures, to get Link out of his face. Wave after wave of these things attacked Link, until Link was able to defeat every one of the monsters in one wave. Promising to make Link pay, the Grim Creeper escaped. Continuing on, Link picked up the Nightmare Key by pushing two blocks together.

Link couldn't find anything else upstairs, so he tried once again to obliterate the last pillar. He was finally able to reach the pillar with the crystal ball by various means, and threw the globe at the last remaining support of the top floor. With a rumble the pillar crashed to the ground, and the top floor of the tower fell into the third! Link climbed back up to the third floor and saw that the pits were now filled in with the remnant of the top floor. Using the hook shot to access a ledge, Link went outside and climbed a ladder to the very top of the Eagle's Tower.

The Grim Creeper stood at the top, and promised that this time he wouldn't hold back, but would make Link wish he was never born! A huge bird, the Evil Eagle, flew overhead, turned around, and picked up the Grim Creeper. Link took out his sword and shield and got ready to fight. Link struck at the eagle when it flew overhead, and when it flew too high he used the Hookshot. Sometimes the eagle would charge him, but Link anticipated his movements and hit him with his sword. The eagle alternated between these two attacks and one other one: flapping with all his might, the eagle would blow a strong wind, and his sharp feathers, at Link, trying to knock him off the tower. But Link put his shield in front of him to block the feathers, and pushed back with all his strength.

It took many blows from Link's sword to destroy the Evil Eagle. When the bird was finally gone, the Grim Creeper said that Link would be lost if the Wind Fish woke. In his last breath, he told Link that, just like himself, Link was in the Wind Fish's dream. Link climbed back down the ladder and went back inside the tower. A door was now open, and Link jumped down and went through it. He picked up the Organ of Evening Calm, and as he warped outside a voice told him that the music of the Ocarina leads...

Standing at the base of the ruined Eagle's Tower, Link realized that the Flying Rooster had left him. He found the rooster in the Hen House, taking the owner for a nice ride around the coop. Link could see that the rooster was happy in its new home, so he left it and continued on his journey.