I loved it! It was like D&D and Zelda characters combined! A very good story, with few typos, (and I mean like maybe 10 in whole thing). Keep writing! I love it! Nice tie in with Windwaker at the end there. Oocca become the Rito. Going to read the story of the Hero of Lightning now. :)

Link knew he knew how to use it.

That looks awkward...
I suggest you change it to

Link could tell he knew how to use it.

First chapter and things are already spicing up and shits hitting the fan, I love it. Can't wait to continue on

10/10

I enjoyed this. A few notes:

Interesting choice of villains; I managed to guess some of it early but not all.
One of my pet peeves about airships is that they usually aren't really explained; the laws of physics must be pretty weird in this universe.
I thought it was weird they couldn't read things only 300 years old; that points to a level of cultural rot that would require worldwide catastrophes like the Bronze Age Collapse (and even then we can now read those scripts pretty well). Another odd thing is putting TP 100 years after OOT, so that fairly modern cannon are in TP only 100 years after OOT.
Bomb arrows are highly unlikely to be able to hit something a few hundred feet up let alone thousands, so I think this needs some kind of magical explanation as well.
And finally, scale is so inconsistent.
Hyrule has much too large an army for its size and population, as do the Darknuts.
Castle town is almost certainly not so big as to dwarf 20 1mi fortresses, especially if Hyrule is so small and has such a small population - it would need to be like medieval Paris with hundreds of thousands
&c.
That said, I nitpick/worldbuild in the hopes it helps you in your future endeavors and I reiterate that this was a good read.

Wow. What a journey. I have so many things to say about this, but I think it'll fill up at least 5 pages, so I'll sum it up. This was undoubtedly one of the best Zelda fanfics I've ever read. Everything about it was fantastic: the pacing, the characters, the story... I hope to see many more amazing stories from you. Never stop writing, you wonderful person.

Chapter 3
It had suddenly appeared
[Author Intrusion. If it’s vital that we know this story, give a scene break and drop into the flashback. I don’t think there’s any catalyst or need for us to know yet. When there is, you can either have Arnak say “I’ll tell you…” and then make the next chapter the scene or then give us the experience focalized through characters instead of dumped in the middle of a scene that’s already confusing. All of the flashback is phrased as telling from the author instead of a natural course of events lived by Arnak]

parents aren't moving in, are they
[Actually, in the technological/social system the world is in, they probably already live in the same house]

three and a-half feet long altogether
[Without a reference item for scale, this would be impossible to guess at (Buffy the Vampire Slayer toyed with this in Fear, Itself)]

which Link demolished behind them
[Why not just block it off?]

Zant had forcibly held
[Interrupting a present-tense scene for repetitious backstory]

movement seemed choreographed
[The oafs that Jackie Chan knocks around are choreographed, that doesn’t make them more graceful than the improvisational hero]

she hadn't used a sword; she'd had
[Passive, repetition, semicolon]

King Ralis sends his regards
[A pointless pleasantry when they’re still in a combat zone and time is of the essence]

saw many unfamiliar creatures flying over the city, dropping bombs
[This is what we already know from the radio…er…‘gossip stone’]

but they may have come
[A lot of talking when military leaders through history tended to expect an aloofness. More of her thought processes should stay in her head. She’s a leader, people expect her to make a decision, not put up everything for a vote]

I perceived the vision
[That’s some convenient Deus Ex Machina]

not entirely certain he could quickly find
[This phrasing is good if you want to slow down tension and distance the character from action or a decision, but not if you want to hold up the tension. If you need us to see the ‘actions that came before’, drop us back into the story THERE and then advance to this point]

While I like alternate interpretations or continuation stories, and you do a fair job of introducing a differentiated character in Arnak, you have a LOT of author intrusion, Telling not showing, and passive sentence construction. I think a lot of this could be fixed if you picked a single focal character and dedicated the scene so all details could only be things THAT character perceived. Not doing so makes it easier for you the writer to lose track of who you're giving information from, tempting you to throw any down any information that crosses your mind.

The reason the city lowlifes avoided the man was this
[Backpedaling. Withholding information from the audience gets awkward, even most murder mysteries tend to use romantic or other subplots to distract the audience from the fact that the detective still hasn’t found the murderer. If a detail becomes observable or important, it’s good to give it to us as it becomes identifiable – that also prevents dumping a lot of data at once]

threw back his hood
[Now his face is visible, but we don’t get any description of it]

well-cared-for but
[This is not visible, and there is no event or action making the detail of his sword’s state important. Part of “describe as the story goes along” is to spread out information so we don’t have data dumps]

saying something back
[Does this mean he can overhear the conversation?]

Uninterested in their conversation
[But you TOLD us that his intention was to find information, so he should be scoping any source possible]

Telma concealed her surprise, but it was obvious she recognized
[Telling. You have a LOT of this, but given the narrative voice and focalization some of that is unavoidable. However, you should Show concrete details whenever possible because 1: that gives us a scene we can follow and 2: you are less likely to contradict yourself when there is little to no telling. With telling you are almost guaranteed to double back and forth]

"Do you see
[Whenever you jump to a new scene, it’s important to identify the Where and Who (and How if time-jumps or travel happen in your story). Starting with dialog drops us into a vague white space without even details to make contextual sense of what’s said, making us go back to the dialog when we finally get enough to start placing who says what]

"No, but I'll
[When you have an established scene and the fact that there are only 2 characters that could speak you can jump without identifying character (I still think it’s a good idea to do so because it helps bind the characters to each other and their environment) to use actions or descriptions to identify a paragraph’s Agent. When introducing you need to give these descriptions FIRST]

but of drastically different build
looked used to adventuring
[Vague, nondescriptive. Give something concrete, something that engages the senses. Even Gooshie from Quantum Leap was described as having bad breath and he only appeared in a couple episodes]

schedule had cleared
[The “had/was/were verb” construction is weak and passive, the existence verbs being something you want to avoid in general]

Link had, of course
time he had
Midna had been with
They had explored
Shad was standing
pocket' Midna had created for him [Others call this Hammerspace]
She had explained
[passive]

store…somewhere on his person
[Which is entirely possible. I’ve seen some very good farnart of Link from OoT with full complement strapped to his back, arms, legs, and torso]

…reverie by Shad's enthusiastic ramblings
[This is a rare instance of Telling that is appropriate. It’s short, moves us past the words, and acknowledges that unimportant words are said but doesn’t waste letters on things that don’t change plot, character, or setting. A good scene should work on 2 of those 3]

executing the skill known
[While the game was interesting, remember that a narrative, a novel is different. You work in one medium and the tools that worked in one do not always work in the other. Referencing game mechanics, for instance, are something you should avoid unless you’re writing a parody]

Why the thing sold items its people couldn't use
[Gameplay and story segregation. Again, I’d avoid mentioning game mechanics]

Oocca were wandering
[wandered]

Link had never
Midna had found
wished they had parted
that he had heard
[passive]

and he told him so
[Not giving dialog is difficult for good writers, but avoiding dialog like this where it clearly happens is cheating the readers. It also denies you to put your own interpretation of Link into the story, making him a shallow cardboard cutout instead of a fleshed out character]

handed the ancient rod…about three feet long
[When something is introduced to the story you can describe it. Skipping it even for moments can disrupt the flow of your scene. As this is a fanfiction and you explicitly state the game it derives from, you could skip description to indicate things are exactly like the game. If you don’t (which is not a bad idea, it allows you to tweak items and environments to better fit your vision of this story world), then you need to go right into concrete details that ground us by using the senses]

doors proportioned for creatures our size
[They’re actually set for creatures even bigger than Link]

…Gossip Stone…which was buzzing insistently
[So you gave him a cell phone…That’s either sad or hilarious, but at least it’s in-universe consistent]

There was a loud noise
[Telling. What specific, something low and resonating like hollow wood? Crumbling stone? Ringing metal? Whooshing air?]

Also, this story now has cover art! To see it, go to my profile and click the link in the note about this story there. Much thanks to the artist, Silverwolf05, who has done quite a lot of art for this story, as well as several of my others.

Chapter 2
Zelda winced in pain
[Wait, they display images too? I thought it was sound only. If it’s anything other than just words, we need a description of that as soon as the (observable) detail comes up to the viewpoint character’s senses]

had landed safely
[None of those areas are in eyeshot of the canon. Also: passive construction]

wasn't powered by Rupees anymore
[Gameplay and story segregation: costing rupees was a balance mechanic that I can’t fathom a good ‘real world’ reason for, so I wouldn’t have mentioned it]

and it was heavy
[While full plate mail isn’t light, it’s tailored to the person and weighed below 15 kilograms. For comparison, modern soldiers pack between 30 and 60kg full field kit. If he still thinks its heavy, he hasn’t been training in it when feudal knights would (and hence retained a lot of agility)]

and started for the surface
[In the armor heavy enough to encumber him on land? I’d think he’d switch to the zora armor to improve his swimming]

him; it was fighting
[, it – semicolons are used to separate two whole ideas that are better joined by a comma to emphasize their link or separated by a period to emphasize their individual fact]

The attack had begun suddenly
[You dropped into some passive before, but we still don’t have a concrete viewpoint and this then kills the scene because it’s very Author Intrusive Telling, passive construction]

Arnak had drawn
[Not just past but passive, too much in close proximity. It’s easy enough to jump into where they are now and describe the who doing what]

She wasted no movements, the sword in her hand leaping unpredictably
[If she wastes no movement, her movement is predictable. That’s one of the things that makes capoeira so hard to follow but also hard to keep up]

He slung it into another wall
[Housing insurance is going to drive people to the countryside]

using his hands and feet
[If he’s using hands and feet when he’s got a sword to give him reach, he’s losing. The invention of weapons was to keep the enemy from getting close enough to bruise your knuckles]

Hero's Shade, an ancient Hero who
[You drop into explanations and backstory so often it’s hard to follow your story. Tell us what’s happening, don’t keep interrupting to throw in what already did, especially when it’s part of a common background your audience probably already knows]

Maybe you'd better listen to what the Sages
[So in other words her appearance was pointless]

a fourth piece
[One piece to rule them all? Or at least sell additional royalties?]

Reading this amazing story again since I just finished Twilight Princess HD, and I couldn't help but wonder why Link never had a fairy in a bottle with him. I mean, they're supposed to save him from dying, I would think that he would have at least one available for things like this. I know that having Link meet the other Heroes and the Goddesses was important for the story, I'm just curious why he didn't have that particular backup plan. Also, shame that there weren't any edits to account for the events of Skyward Sword.

Well. I must say. From the time I had found and lost this fanfiction probably four years ago, I am thrilled to see its completion and even more so to read it to its end. Erik's death has devastated me, but it was in no means bad. It was a satisfying character death, and I am seriously going to miss him. Correct me if I'm wrong but I think I saw a sequel to this beaut in my searches for it, and I have to say that I look forward to the time I will read it if it exists and if I'm not crazy. All in all I loved the story, I loved the plot, and I hope to discover more of your work in the near future when I am not an emotional wreck over Erik lol. Keep up the good work.

He was already powerful before, but now a dark master sword? Where are all this swords coming from?

Wait, what did Ilia tell him? I want to know.

I bet nemo is salty at the moment. He couldn't get the triforce of Shadow to work for him. Wonder what conditions it requires it to.

Shadow Link? This story isn't pulling any punches and I love that. Also like the pacing.

Daaawww, it ended in a hug, but that thing is still on the other side though, so that's a problem, and now some guy is looking for the Master Sword. But I thought only Link could pull it off, so i don't know why he's even going for it.

I like that the events happen fast, but no so fast that details are missed out.