Come on people! It can't be that bad!

Chapter Five: Back in the present

Link smiled, finally recognising the instrument as an Ocarina, and while he was holding it, he noticed it had the symbol of the Triforce on it. He wondered if this was the Ocarina his Grandmother had mentioned. Looking down at the desk, he saw some diagrams and notes on a piece of paper; one diagram was of the Ocarina that Link was holding, and was labelled.
“Ocarina of Time…” Link murmured to himself.
Link saw some music notes on the desk on a separate sheet, which was labelled: ‘Song of Time’ and below it, a message: ‘Used for travelling in time’, and below that, in Tetra’s elegant handwriting: ‘Must use Ocarina of Time’.
Link, curious as always, blew into the Ocarina of Time, and began playing the Song of Time, thinking of back before his adventure started. When he opened his eyes, he saw that he had not gone home, and the only time that had passed was that which had gone by when Link was playing the song.
“It’s not gonna work y’know,” said a voice,
Link turned to see Tetra leaning against the doorframe.
“What’s not going to work?” asked Link,
“The Song of Time,” said Tetra, matter-of-factly,
“Why not?”
“Because that isn’t the real Ocarina of Time, I made it, the real thing was lost when Hyrule was flooded.”
“And you didn’t recover it while you were in Hyrule because…?”
“Well I didn’t know it existed then now did I?”
“Suppose not.”
“Get out of my room.”
“Okay…”
Link, defeated, put the fake Ocarina back on the desk, and went below to the storage deck. In here were several crates, several of which contained many of Link’s treasures, equipment, and other miscellaneous items, which he couldn’t carry around with him.
Link made his way to the far side of the storage deck, where his old boat, the King of Red Lions, the once enchanted boat that had aided Link on his first adventure now leant against the wall.
“That really was a wonderful rendition of the Song of Time, young one,” said a voice,
“Wh- who’s there?” Link asked, looking in all directions,
“Link, I haven’t been gone that long, you should at least remember my voice,” and at that, Link suddenly recognised the voice.
“Your Highness?”
“Yes, it’s been quite some time hasn’t it?”
Then, the King of Red Lions, dormant for almost half a year, began moving once more.
“You survived?” asked Link, incredulously,
“No, young one, I did not survive,” was the reply,
“But, you’re speaking to me, so… what do you mean you didn’t survive?”
“I did die, but dark clouds have been forming in the spirit realm, and when you played the Song of Time, I was brought back to the Realm of the Living, but as my body had perished, I had to claim this boat as my body, or forever be cursed to walk the flooded waters of Hyrule, like my compatriot of the Cobble Kingdom, Mutoh.”
“So, you’re alive, but you’re a boat now?”
“In a sense, yes.”
“Well, I’ve been summoned to a new adventure, and you’d be a help,”
“Young one, I would be honoured to continue my adventure with you, now, take with you the equipment you may need, and any other items, and we will exit from here,”
“Yes sir!” Link exclaimed, lifting himself from the floor, and he hurried off to open his crates.
After taking some time finding his equipment, he had some trouble choosing which things he might need, but he had several variations of some items, so he chose the stronger ones. He chose the Mirror Shield, the Skull Hammer and the Boomerang, among other things.
Once Link had gathered his things, he realised he did not have a sword, as the two more powerful swords he had once used were gone, and his normal regular powered swords had been returned or lost. Unperturbed, as always, he searched through a crate until he came to the back and found what he was looking for, an hourglass.
“Ready sir.” Link said, as he came back to the ship,
“I see you have gathered some new equipment,” said the King of Red Lions,
“Yeah, but I don’t have a sword.”
“No matter, we shall acquire one in due course, now onwards!”
And as he said it, the side of the hold of Tetra’s pirate ship opened up and became a ramp to the Sea.
Ignoring the shouts of protest, annoyance, and downright fear (guess who), Link pushed the King of Red Lions into the sea, and then jumped in.
“Link! I thought you said you weren’t going to travel in that ship again, on account of it not being alive anymore!” was a cry from above, which turned out to be from Niko,
“Well, you’re not gonna believe this…” was Link’s reply.

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Credit to the awesome Ranil for the sig and the avatar.
My timeline theory