The planet Krypton, normally a peaceful place, has recently been ravished by a great war, sparked by the evil Lord Brainondorf.
Brainondorf being after the mystical Triforce, would stop at nothing to get his hands on the mystical artifact. Hearing the pleas of the population, Din, Ni-rao, and Farore, the gods of krypton, decided to protect the Triforce by destroying the planet of krypton and sending the Triforce in pieces towards a backwater planet named Earth, hoping to kill the evil Brainondorf in the process.
However Brainondorf, a being of class-12 intelligence, decided to seal himself in the mystical land of Hyrule, shrinking it as to avoid being destroyed, and drifting towards earth, sealed in a bottle for protection.
Coincidentally at that time, a loving couple Jor-El and Lara Lor-Van, had a young child named Link-El who, unknowing to the parents, had a mysterious Triforce-shaped birthmark located on the back of his left hand. Jor-El realising that Krypton was collapsing around him, sealed young Link-El in the Temple of Time in order to protect him from any dangers.
Seven years later the bottled land of Hyrule lands in a mysterious forest named the lost woods. Baby Link-El is transported from his imprisonment in the bottled land, by the incredible birthmark, to a small forested town named Kokiri-ville where a nice couple adopt him thinking him human.
Meanwhile in the bottled land, Brainondorf has escaped the bottled land and has decided to lay low until he can find the location of the Triforce.
He has decided that while waiting he would go and absorb all the information he can from the Earth while putting himself in a position where he could quickly learn the whereabouts of the Triforce while not drawing attention to himself.
Jumping ahead 10 years, young Link-El, now named Clark Kent by his Kokiri-villeian parents, now goes to school and has befriended a beautiful girl by the name of Sarana Lane. One day while trying to get a date with Miss Lane, Clark is drawn towards the Lost Woods where he is surprised to discover what appears to be a miniature model of an amazing land. When he reaches to grab it, the birthmark on his hand begins to glow yellow and he suddenly finds him self in a amazing and yet familiar temple. While exploring the temple young Clark finds a sword stuck in a pedestal.
As though a voice was telling him what to do, Clark steps up and grabs the sword pulling it out of its pedestal. Clark suddenly finds himself in an unknown place facing two people he has never met, those people were Jor-El and Lara.
They tell Clark all about how he is there, himself, Krypton, Brainondorf, and the Triforce, they also train clark, so that if he is to ever fall into any trouble he can get himself out. When Clark asks about the sword, his parents only tell him that it is called the Master Sword and that it was crafted by some mystical sages and is said in legends that the destined hero will one day pull it out of its resting place and use it to banish Brainondorf.
Later they tell Clark that it is time for him to leave and that if he ever wants to talk to them, he is to return to the Temple of Time and place the sword back in its stone. Suddenly Clark finds himself back in the lost woods holding the Master Sword but something is wrong. Clark notices that the area has a darker tone to it, and not only that, he feels like he is taller, bigger, and more mature.
While pondering this problem, Clark is distracted by a glowing piece of what appears to be yellow metal. As he approaches it, the bottom-right triangle of his Triforce birthmark begins to glow, when Clark touches it he suddenly finds that he now knows what he must do.
He knows that there are six more pieces like this and that they will complete what is called "The Triforce of Courage" and that great challenges lie ahead. As he was leaving the forest he was shocked that he could hear screaming far into the distance even though there was nobody near by.
While running towards the screaming, Master Sword in hand, he is shocked when he suddenly begins to run at incredible speeds. It appears that the small Triforce piece has given him super speed and hearing as well as knowledge.
Meanwhile Brainondorf has already recovered the full Triforce of Power and is now on a quest to uncover the other pieces of the Triforce.
With the Triforce of Power in hand, he has taken the world and is feared wherever he goes.
Currently, on his quest to uncover the rest of the full Triforce, he is attacking a village where he knows a piece of the Triforce of Courage is located. Unable to locate the piece, he decides to leave in order to formulate a plan.
Seconds after he leaves Clark arrives to see what the problem is. The people tell him that Lord Brainondorf has attacked and that all their problems started the day a meteor hid the middle of the city carrying a yellow piece of metal.
At these words, Clark asks to see this metal and the villagers take him to it, as he approaches it two amazing things happen. First thing is that the Triforce on Clark's hand reacts and begins to glow, the second thing is that the meteor rocks surrounding the piece of Triforce start to glow and cause Clark great pain.
During all this Brainondorf sees this and realizes that a Kryptonian must have survived and not only that, this Kryptonian must be the hero of the legends as he carries with him the mystical Master Sword from the Temple of Time located in Hyrule. As Clark backs away from the meteor rocks he asks the villagers if they have anything he could use to get this piece of Triforce without feeling the effects of the rocks.
The villagers all get together and give him a whole list of supplies from a slingshot to a bow, a spring-loaded grapple, and a lead lined silver shield that amazingly did block the effects of the rocks.
Using the shield to cover himself, Clark recovers the piece of Triforce and amazingly in a glow of light, gets a change of clothes. Clark is now dressed in a classical Kryptonian uniform of a green tunic and hat with a scabbard for his sword and a place for his shield.
As he goes to look at his reflection in a lake, Clark coughs in shock and amazingly his cough blows a tree down and also blows Brainondorf away. Clark does not notice this due to the shock of seeing that he is years older.
It appears that by taking the Master Sword out he had traveled forward in time seven years.
After amazingly placing all the supplies given to him into a bag that was given to him by the Triforce, with room to spare, Clark ponders about how his life had changed so quickly in, what was for him, a day, but in reality was many years, and that how it appears that each piece of the Triforce of Courage is giving him new powers.
He recently learned of a new power to burn things just by looking at them as well as an amazingly super breath. As he decides to leave the village to find the other five remaining pieces, a villager stops him so that they could give him a gift for ridding them of the cause of their troubles.
They give him a red cape with a full Triforce picture on it. Clark thanks them and leaves back towards the forest having made up his mind that he would put the sword back into its pedestal to talk to his Kryptonian parents again. As Clark makes his way to the Bottled land of Hyrule, he is being watched by two people.
One of the people is Brainondorf, who has realised that he is the bearer of the Triforce of courage, the son of his Kryptonian adversary Jor-El, and one of the keys to getting the full Triforce, with a glance at the Triforce mark on his hand he leaves to his castle in Metropolis or what he likes to call New Hyrule.
The other, a woman with a similar mark on her hand with the bottom left Triforce piece complete. Knowing that she has found the third bearer of what she called the "triangles of power", she smiles and also leaves back to "New Hyrule"