Originally written by Nintendo on its old website of zelda.com
When Hyrule was created by the three goddesses at the beginning of time, there were certain side effects of its creation which Din, Nayru and Farore did not anticipate. As the three holy women breathed life into the world and chased away Emptiness, their potent breath slipped through tiny cracks in the folds of space and created millions of alternate worlds in the process.
The goddesses were not upset by this. In fact, they were quite amused at the possibility of watching millions of dramas unfold rather than just one. Each world, they noticed, shared common elements but also differed in major ways. One of these worlds, called Termina by its inhabitants, is where the legendary tale of Link's second great adventure began ...
On a dark and dreary afternoon, a lonely Skull Kid sat at the base of a tree and cried about his pitiful position in life. With no friends to talk to, he sat there weeping as a steady rain soaked his clothing and dampened his spirits. He was beginning to think that he would never cheer up when two feisty fairies named Tatl and Tael happened to buzz by.
The two fairies, who happened to be brother and sister, decided that Skull Kid would make the perfect playmate. This greatly improved Skull Kid's mood, and the three became fast friends and were immediately inseparable.
The happy times lasted for a long while, but eventually things took a turn for the worse. One day, Skull Kid "borrowed" an interesting mask from a traveling Happy Mask salesman. He didn't mean any great harm,and perhaps he even intended to give it right back, but little did Skull Kid know that the mask he had just swiped was the legendarily wicked relic known as Majora's Mask.
When Skull Kid tried on Majora's Mask, he was instantly overcome by the evil power of the mask. Skull Kid had always possessed a mischievious spirit, but while wearing the mask his pranks became more hurtful and mean-spirited. Tatl and Tael were worried about Skull Kid's behavior, but they couldn't resist tagging along with Skull Kid to see what he would do next.
Back in Hyrule, Link had just defeated Ganon,the King of Evil. After traveling through time to return to his younger days, Link set off on a personal mission to search for his missing fairy friend, Navi. Although he was proud of his accomplishments, his soul felt empty without his loyal friend Navi to share in the victory.
Just as Link was feeling particularly low and alone, he experienced an unexpected encounter. Through some magical force unleashed by Majora's Mask, Skull Kid passed through an inter-dimensional portal and made the leap from Termina to Hyrule. Unfortunately for Link and his trusty horse Epona, he and his steed became the unwilling targets of Skull Kid's mischief.
Skull Kid threw Link from Epona, stole the Ocarina of Time, and led the young hero on an extended chase. Link had just lost one friend, and he wasn't about to lose sight of another. His loyalty to Epona was so strong that he followed Skull Kid all the way through the inter-dimensional portal and found himself in the odd world of Termina. Link was able to catch up with Skull Kid, but Epona was no where in sight. To add insult to injury, Skull Kid jinxed Link by imprisoning him in the body of a wooden, plantlike creature called a Deku Scrub.
Forced to cope with his strange, new form, Link the Deku Scrub also had to deal with a newly-forged alliance with Tatl. The fairy was separated from her brother by the careless actions of Skull Kid, so she reluctantly agreed to guide Link through Termina -- where everyone was a stranger, yet each individual looked like the twin of someone Link had met in Hyrule.
The center of the parallel world was Clock Town, where a towering clock reached into the sky. Link quickly learned that Termina was in great peril due to Skull Kid's trouble-making ways. Everyone's life was in a state of disarray, and the very moon was on a collision course with the world. Link discovered that in three days, that the moon would crash into Termina and kill every last inhabitant.
The first to greet Link when he arrived in Clock Town was the Happy Mask salesman whom the Skull Kid robbed of Majora's Mask. The mysterious businessman struck up a deal with Link: If Link could find his Ocarina and use its power of time travel, the salesman would return Link to his original form, lifting Skull Kid's Deku Scrub curse.(By playing the Song of Healing)
Link was able to recover his Ocarina, but he had still not found Epona. Also, after learning of Termina's troubles he decided that he had to do something to halt Skull Kid and his unruly actions.
Using the power of magical masks like he had never seen before during his adventures in Hyrule, Link was able to assume the identities and powers of other characters like a Zora and a Goron. Though he put forth a heroic effort, three days was simply not enough time to right Skull Kid's many wrongs and stop the descent of the moon.
Link used his Ocarina to relive the same three days again and again, and was eventually able to change the courses of people's criss-crossed lives. After facing many tests of strength and courage, the Hero of Time was even able to free Skull Kid from the evil power of Majora's Mask and quiet the wrath of Majora itself.
Once again, unfortunately, he was unable to share his victory with Navi.
At this point, it was no longer necessary for Link to relive the three-day cycle which he had come to know so well. His spirits were lifted by experiencing new days and nights, but deep in his heart he was still saddened by Navi's disappearance.
Link had many more adventures in the land of Termina, but eventually his heart led him back through the inter-dimensional doorway to his homeworld of Hyrule, where he went to live a normal life.