Well, I wrote this in, what, 20 minutes, so it's bound to suck. Also, this is, like, based on a conversation between me and my friend, so...yeah. Enjoy. :p
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Part One:
How It Happened...
It was only once through all the years of Hyrule did a Hylian ever see a short man in a red hat and overalls galloping unsuccessfully on a beautiful horse with a stunning white mane. “Are you a deformed Goron?” was the only question asked to the plump man, although it was only answered with a weak punch to the interrogator, knocking the questioner unconscious. However, it was soon enough that a young woman with dazzling red hair recognized the horse, and Malon knew Epona’s owner was not riding on her.

She chased after Epona, but the horse was just too fast for her, and the sun was starting to set. Malon ran back to the ranch for if she stayed out in the dark too long, children from the underworld, known as Stalchild, would come out to play, and any mortal in their sight was bound to be gone the next day. As she drew nearer and nearer to Lon Lon Ranch, she saw a young man in a rather unstylish green tunic she had known for a very long time.

“Fairy boy!” Malon exclaimed gleefully, but the man in the Kokiri boots had been knocked unconscious. However, he had no bruises or wounds, except a black eye. Malon grew worried, and she called for her uncle. “Ingo! Come quick! Link is…Link is…LINK IS DOWN!”

Never once had Malon addressed the young man as his name; ‘fairy boy’ and ‘Link’ was the same to her. Her uncle realized this and was concerned of the situation. He called for his brother, and Ingo ran to where Malon was, with Talon tumbling after.

“What happened?” Ingo asked Malon. Malon pointed to Link and Ingo’s eyes slowly moved to the still body. Huffing and puffing, Talon came out of nowhere with a pocket egg. “I…I…thought…this”—he paused—“would help…” he managed to cough out. Malon examined the egg.

“But Daddy…” Malon said. “These eggs don’t hatch until the new day!” Talon hadn’t heard a word she said since he had just fainted of exhaustion; after all, he hadn’t ran that far in who knew how many years. Ingo decided his brother couldn’t be any more helpful in the situation, so he took the pocket egg and told Malon to bring a candle. Malon soon returned and Ingo set the egg above the tiny flame. It quickly hatched, and the Cuckoo inside it cried its traditional scream. Link and Talon rose immediately.

Malon helped Link into their house and gave him two bottles of Lon Lon Milk. “Link,” she quietly said, “what happened?” Link almost choked on the milk. He was stunned to hear his name – his actual name – in a serious tone from the happy girl who had always called him ‘fairy boy’. He decided not to question it and began to tell the three of all of the events that had recently happened to him.

“It’s Mario,” Link started, and the three stared at him. He explained to them that Mario is this Italian plumber in a red cap and overalls, and he looks like a deformed Goron.” They understood immediately; Malon even claimed to have seen him. Link continued his tale.

“I met Mario in 1998, when we were both scheduled to be in the same game, Super Smash Bros. 64. However, it was the same year that this game – Legend of Zelda: Ocarina of Time – was named Game of the Century. Being the mascot for Nintendo”—Link decided not to explain Nintendo to the trio, fearing it would confuse them even more—“Mario was exceptionally jealous that Super Mario 64 was not Game of the Century, and that my game was, and to make things worse, I was in a popular game with him. So he has decided to ambush me and show what he and the Mushroom Kingdom is truly made up of.”
[CENTER]~ * * ~ * * ~ * * ~[/CENTER]

The man who Link identified as Mario was riding on Epona, but it seemed with every step Epona too she injured him, which she seemed to enjoy. However, neither realized a blue fairy madly charging at them. When the blue fairy caught up to them, she cried, “STOP!!” Epona came to a sudden halt, almost throwing Mario off the horse. Navi pointed and laughed at Mario, then started speaking.

“How, may I ask, did you manage to ambush Link, as well as convince Epona to come with you?”

The tubby man laughed. “I’ve played this game before, I know what to do. I used a grasswhistle to play Epona’s song…how else would I get her?” Mario said. “And let’s just say Link was knocked out by an unidentified boulder.” Mario turned away and whistled.

“Whatever,” Navi said, as she decided not to question this. Less talk from the fatty in red is good, she thought to herself. Plus his Italian accent is terrible and is killing me. There was just something about him that made her say, “I can trust a deformed Goron like you, I guess. After all, you pretty much know what to do.

“Do you see that sack around the horse’s neck?”

Mario nodded.

“Well that sack has three special stones, the—”

“Kokiri Emerald, Goron Ruby and Zora Sapphire,” Mari finished. “I told you I’ve played this game before.” Navi game him a dangerously evil and warning look, telling him not to butt in anymore before she continued.

“Anyway,” she said, “Link had gathered the three stones and put them on the pedestal and took the Master Sword and did all that junk. After he was an adult, he took the three stones and replaced them with phonies, planning to make huge rupees off them. Do you know how many rupees those cost?!” she asked Mario. He shook his head. “7000 rupees! 7000! And I hear Ganondorf is willing to buy them for 30 grand each!

“That’s why we have to go to the castle to sell them. Say we split the profits 50-50?” Mario opened his answer to speak, but Navi didn’t give him the chance. “Oh, you’re so kind! I’ll keep all the profits, if you insist!” Mario frowned, but he was too afraid of Navi to argue.

She took a long look at Mario.

“The guards won’t let you in the castle, I can tell,” she said finally. “But, no worries! Link was supposed to go to the castle to give the princess a special-made Goron bracelet at her request.” Navi lowered her voice. “I hear she’s training for the newest Super Smash game, since she was such a waste in the original one.

“Unfortunately, Link currently has the bracelet in his possession, but in his sack, there’s a signed letter from the princess. Normally, I’d sell her autograph, but we need it right now. So, get the letter out”—Mario rummaged through the sack—“and remember not to lose it.”

Mario just nodded, as he did not understand most of what Navi had just said. Navi sensed an aura of stupidity around him, and thought to herself, Gee, what a dunce!

She pointed to the castle. Mario looked there, and asked, “Why?”
Navi had lost her temper, She picked up Mario by the collar (of his new red polo) and threateningly replied, “Go—see—the—princess. Now.” As Mario reluctantly agreed, he noticed he had developed a fear towards the flying blue thing.

The trio traveled across Hyrule Field. They weren’t very far from the Hyrule Castle when suddenly, the moon was in place of the sun. “Oh boy,” Navi said, and from far away, she saw the drawbridge to the Hyrule Marketplace close, and Stalchilds emerged from the ground. Mario knew what to do, and he quickly looked through Link’s arsenal pouch and pulled out…

…the bunnyhood mask!

He stuck it on his head, and as he did, they all disappeared. “Good thinking!” Navi complimented him. They continued to pursue their mile-and-half distance, with Mario wearing the mask.

As they kept moving, a man who was running very slowly (“at an average of 4 miles per hour” according to Navi) happened to come across them. “I am the running man of Hyrule,” he introduced himself, “and I happen to like your mask. How much you want for it?”

“Five hundred rupees,” Mario said to him. The running man gave him 1000 instead. With the bunnyhood mask on, he ran 200 miles per hour, “increasing his speed by 500%!” Navi said. Mario smiled at his ingenious accomplishment of profit. Navi greedily looked in the huge sack of rupees.

“You idiot!!” she exclaimed. “They’re fake!”
“Come back! You gave me the wrong kind of rupees!” Mario called the scammer, but he was already long gone. To add to his troubles, the Stalchilds came up again, much to his dismay.

Mario grabbed the heavy Biggoron Sword from its scabbard and attempted to kill them all, but the sword did no damage to them. “Oh yes!” Navi remembered. “Zelda put a spell on them so they would kill all intruders!”
Navi thought a while, then said, “Use the Master Sword instead.”
Mario fended off the Stalchilds and stuck the Biggoron Sword where it belonged, but he looked in the arsenal pouch for the sword. Navi exasperatedly cried, “The scabbard, man, the scabbard!” Mario kept looking through the arsenal pouch, not knowing what she was talking about.
He suddenly shouted, “LOOK! I found Farore’s Wind!” The green jewel glowed mystically as Mario threw it down and was greeted with options.

“Would you like to set a warp point or teleport somewhere?”

Mario selected the teleport option.

“Please select the destination you’d like to find yourself at. This requires 10 magic power.”

He hit ‘Hyrule Marketplace’ dot, but they didn’t go anywhere. “You only have 3 magic power, dummy,” Navi said. He looked around for a solution, and strangled a Stalchild for 10 MP. Once again, he selected the ‘Hyrule Marketplace’ dot.

The horse, Navi, and Mario were taken to Hyrule Marketplace. “I never knew there’d be so many people here at this time of day!” Navi said. However, Mario and Navi couldn’t get through because of a Hylian mob surrounded around them, demanding where in Hyrule did he get that awesome polo and how much it cost. Mario, who was unsure what to do, hopped on Epona and pointed to the Temple of Time. “THERE!” he shouted. These old guys are selling them for half a rupee!” As soon as he said it, they took off like crazy. Even Navi flew to the Temple at jet speed, but returned shortly, addressing Mario as a brilliant liar.

He made his way towards the castle, but remembered the guards. Navi was at the black marketplace of Hyrule, trying to sell the stones, so Mario could remember what she told him. Fortunately, for Mario, a clothing shop stood in front of him. “Take any costume for 200 rupees,” Mario read. “But, I only have twenty,” he thought to himself. Suddenly, he remembered the fake rupees and took a good, long look at them.

They did look real.
And the store owner could fall for it.

And how could you tell, really? The real ones were just a little heavier. Even Mario could barely tell the difference. It was worth a shot.

Mari entered and looked around. “Excuse me,” he asked the shopkeeper. “Do you have a Hylian guard outfit?”

The manager looked up, looking at him suspiciously. “Why in Hyrule would you need the Hylian guard costume?”

Mario thought a while. “Well, I am in need of a, emmm, a Halloween costume,” he said, unsure of what that meant. He’d seen it on TV before, so it had to mean something.

“Ahhh, Halloween. All the kids in Kakariko are doing that these days. You’re my first to buy a Hylian guard costume, my boy,” he said, looking through the racks with him. “Here it is. It’s special edition, so take care of it. Return it, and you get half your money back.” Mario gave him the rupees, and sped out of the store.

“Do I really look that young?” he thought, remembering how the words “kids” and “boy” were directed at him. He also noticed the shopkeeper didn’t come after him. Just to double-check, he stopped and checked his wallet.

“DARN! I gave him my real rupees!” Mario thought about his mistake, since he only had 20 to begin with. Why did he still have 1000 fake rupees?

Navi met up with Mario. “The black marketplace didn’t go so well,” she said. “Ganondorf is currently busy scheming his evil plans, so that’s a bummer. What did you do while I was gone?”

Mario explained to Navi what had happened. He also asked her about his situation.

“Simple,” Navi said radically. “You obviously forgot one zero, you idiotic Italian. Now move,” she ordered, “We’ve got some stuff to do.”

Mario was a guard now, running off on a horse. He was going through the castle rather smoothly, until he got a cut from a flying rock. He looked in the direction of the attack, but he only saw a flash of a green hat—pointed, elfish, and unstylish—before the culprit disappeared behind the hedges. Navi thought to herself, There’s only one person whose aim is that good.
After some more smooth traveling, Mario finally made it to the Castle Courtyard, where Princess Zelda seemed to be awaiting a guest.
She was playing her ocarina beautifully, but as soon as she heard footsteps, she abruptly stopped. “Link,” she said, “what took you so long?” She turned around.

“What in Hyru--! Who—or what—are you?!” Zelda shrieked.

“I’m—I’m a guard, I swear!” Mario said, with his hands up. Navi shook her head. Way to give it away, stupid, she thought.

“I know you’re not a guard!” Zelda said. “I put a spell in this area so guards wouldn’t come in!”

“I guess I’ve been framed, then,” Mario said, grinning evilly. He was probably trying to grin evilly, but it wasn’t turning out well. He took off his disguise.
“They call me”—he paused dramatically—“Mario.”

What an idiot! Navi thought, thinking how terrible his dramatic pause was.
The princess gasped, then pointed off somewhere else. “Look, it’s a Goomba!” she cried.

“Where?” Mario asked, turning around frantically. Zelda magically transformed into a mysterious man in tight pants. Disappointed, Mario turned back around.

“Sheik?!” he said. “What are you doing here? I thought you revealed yourself a long time ago, Zel—”

“I’m not Zelda!!” Sheik said nervously. Then, he got back to business. “What happened to Link?” he asked. “He was supposed to bring the princess her Goron bracelet!” Sheik used his chain to bind Mario so he couldn’t run away.
Mario broke out of the chain easily and seemed very amazed.

“If you’re not Zelda…” he started slowly. “How…HOW DID YOU ABDUCT ZELDA AND COME HERE SO QUIETLY WHILE I WASN’T PAYING ATTENTION?!” he excitedly shouted.

Sheik slapped him, and Mario was out cold. Out with a slap, what a weenie! Navi commented to herself.

Then, Link ran into the courtyard with a bunch of guards at his tail. However, once he entered the courtyard, the guards turned around, thinking he had disappeared.

He had obviously been running for his life, Navi could tell, from the way he was breathing. Navi hid in the arsenal pouch that was near Mario. She would hide, for now.

“Zel…da…” Link said, huffing and puffing. “I…brought your… Sheik?” he said, confused. “Have you seen Zelda?”

Sheik sighed. Link must have never found out I was the princess in disguise, he thought. And I don’t want to do that long speech again. He must have dozed off there, that idiotic loser. Quickly, Sheik looked around. “LOOK!” he said. “It’s Kaepora Gaebora!”

Link looked around. “Where?” he asked nervously. Sheik used this time to transform into Zelda.

Mario’s eyes were flickering. He was slowly getting conscious. Link breathed a sigh of relief. “He’s gone,” he said, with a pinch of hope in his voice. “But… HEY! Where did Sheik go? He was just here! Did you see him, Zelda?” he asked the princess.

“No,” Zelda said, a little too quickly. “But I believe,” she said, changing the subject, “that you have something for me.” Zelda smiled.

Link, who was disappointed at the sudden disappearance of Sheik, brightened. “Zelda, here is the Goron bracelet I promised you, made especially for you!” Link dug through the pouch on the belt of his tunic and pulled out a shiny, gold bracelet.

Mario was fully awake. He reached in the abandoned arsenal pouch and pulled out a blue jewel, similar to the one he’d used earlier. He silently went towards Epona to retrieve the Master Sword.

Zelda beamed at the sight of the bracelet. Link handed it to her and tried to put it on. “It’s too small,” she said. “Can you help me?”

As Link was helping Zelda with the trinket, Mario used Nayru’s Love. Heaving the Master Sword, he charged at Link. Link easily dodged the attack, mainly because Mario’s accuracy was very low. Zelda tried using her spells on him, and Link tried to attack, but they both did no good, as Mario was protected by Nayru’s Love, a diamond-shaped blue shell helping him. Grabbing the small arsenal pouch that Navi was in, he reached in and released a Bombchu in the direction of one of the Castle Courtyard walls. The toy mouse flashed red, and it blew up. Mario made a run for it with the Master Sword and the pouch, with Link hot on his trail. He ran out of the castle and dove into the moat, where Link got the Ocarina of Time for the first time. He swam north, then west, and finally laid down on dry land.

All this time, Link was swimming behind Mario, yet he didn’t know. Link hid behind a tree and watch a mushroom-hatted munchkin walk towards Mario.
Mario, who was on the ground heavily breathing from the fatigue of swimming, looked up. There was a Toad looking at him.

“Did you get it?” the Toad asked Mario.

“Oh yes,” Mario replied. “I got it.”
[RIGHT]This is where the real adventure begins!
Stay tuned for Part II out of...??[/RIGHT]
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Just so ya know, Part II isn't due for a long time.

I had a hard time understanding quite a bit of it.

It's much easier to read if you're a die-hard Legend of Zelda fan.