Link is a young boy who lives with his Uncle in Hyrule and is the male protagonist. He finds himself thrust into a quest to save Hyrule after one night when he begins to hear a girl's voice in his head telling him to come to the dungeon of the castle and rescue her. He wakes up to see his Uncle sitting at the table with a sword and shield in his hands. His Uncle tells him to not leave the house and that he will be back in the morning. Once his Uncle leaves, Link disobeys his Uncle's orders and goes to the castle. He finds himself unable to enter the castle due to the guards who prevent him from getting in. He hears the girl's voice again that tells him to follow the flower path that leads to a secret passageway that leads inside the castle walls. He follows the path and finds a hole underneath a bush at the end of it. He falls down the hole and is shocked to find his Uncle wounded from an apparent battle with the guards. He goes to him and his Uncle scolds him for not listening to what he said earlier about staying at home. Nonetheless, he gives Link the Fighter's Sword and Shield that he possesses and tells Link how to use the Spin Attack, a secret technique passed down their people, the Knights of Hyrule. He implores Link to save Princess Zelda and then he falls into unconsciousness. Link leaves his Uncle and enters the Castle. After fighting through many guards and obtaining the Boomerang, Link finally finds Princess Zelda at the lowest level of the castle in the dungeon. He defeats the Ball and Chain Soldier who is guarding the princess and sets her free.

After freeing her from her cell, he takes her back through the castle and they use a secret passageway located in the throne room to reach the Sanctuary. Once Princess Zelda is in the safe hands of the Sage, Link leaves and continues his quest by searching for the wise man named Sahasrahla. After getting directions from Sahasrahla's Grandson, he locates the wise man in a temple located near the Eastern Palace. Once Link obtains the Pendant of Courage from the Eastern Palace, Sahasrahla gives him the Pegasus Boots as a reward for his efforts and tells him to obtain the other two pendants and gain the Master Sword. Link goes on to obtain the two pendants, the Pendant of Wisdom and the Pendant of Power, and ventures into the Lost Woods to find the mythical sword.

Once Link has the sword in hand, he receives a frantic telepathic message from the Loyal Sage and when he arrives to see what is going on, he finds Princess Zelda gone and the Sage wounded. Link discovers that Agahnim is the reason behind these events and sets off for the castle. He goes to the upper portion of the palace that he could not enter before and uses the Master Sword to dispel the barrier that was preventing him from entering. Once inside, Link storms through the dark wizard's hideout, and after many battles, he finally reaches him. Sadly, Link finds him and Princess Zelda too late, for right as he enters, he sees the princess behind sent to the Dark World before him. Link then heads after Agahnim and battles him by turning his own magic against him using the Master Sword. Upon his defeat, Agahnim draws Link into the Dark World, where now the young hero finds himself in a quest to find the Seven Maidens and defeat the person who is truly behind all of the evil events that have been happening, Ganon.

After Link frees all of the maidens from their prisons, they combine their powers together and break the barrier surrounding Ganon's Tower allowing him to enter. After fighting his way through the tower, Link finds Agahnim waiting for him and duels him once more. This time though, Link truly defeats the evil wizard and discovers that the man was actually Ganon's alter ego. A figment of Ganon comes out of the fallen wizard and changes into a bat and flies away to which Link follows to see where it is headed. The bat then crash lands into the top of the Pyramid of Power and creates a gaping hole. Link falls down through the hole and finds himself face to face with Ganon. The two engage in battle and using the Silver Arrows that Link obtained from the Cursed Fairy located inside of the Pyramid, and the Master Sword, Link is finally able to land the final blow to the monster and defeats him. After Ganon's defeat, a door opens behind the battlefield and in the next room, Link finds the Triforce. With some insistence from the Triforce, Link touches it and makes a wish which returns everything back to the way it should be.