Fragment from the History of Hyrule (spoiler warning)

[The Nameless Paradox]

Fragment from the History of Hyrule

The identity of the skeleton warrior is revealed to you after finding all of your skills: He is the Hero chosen by the Gods time and time again. When you get the final technique, Great Spin, the skeleton that has been training you gives you the following speech:
"Although I accepted life as the hero, I could not convey the lessons of that life to those who came after. At last, I have eased my regrets."
Apparently Link can only pass on his own skills to the next hero blessed by the goddesses, or himself reborn.
He also tells you the first time that he meets you that he is the last of his people, and that the skills he is teaching you are passed on from back into his bloodline. A Link to the Past refers to the Link in that particular game as the last descendant of the seven knights that defended the Royal Family, and one that carries the abilities of their bloodline. Besides the courage he carries from his ancestors, it is remarked that he also carries their abilities.
The Zelda series does follow a storyline, (which Nintendo themselves admitted to) and the games take place in a specific order. This particular game is another piece of the puzzle that is Zelda's timeline. Clues like these can be used to piece together a timeline that this series follows.
For instance, Twilight Princess says that the main character of this game, whatever you choose his name to be, wears the clothes and is endowed with the spirit of an ancient hero that once saved the realms, thus referring to the essence of Link instilled in every hero found in each game within the Zelda series. Some of the other factors that can be taken into consideration:

Before Twilight Princess even starts, Ganon breaks out of his seal, but then is banished to the Twilight realm by the lingering spirits from the sages. At the end of this game, Link duels and kills Ganondorf. His breaking of the seal suggests that this game must occur after OoT.

Both Ocarina of Time and A Link to the Past both announce that Link is the last of his bloodline, descending from a long line of Knights. So while the skeleton warrior says that he is the last of his bloodline, either Link from OoT or LttP could have come before Twilight Princess chronologically.

However, Ocarina of Time probably occurs after a Link to the Past. Reason being, several locations that exist within LttP are named after the sages that sealed Ganondorf away.

Another clue is that LttP's storyline starts off by saying that Ganon used the Triforce to turn in what was once the Sacred Realm into the Dark World. Even though it is true that the Dark World reverts back to its glory when Link touches the Triforce at the end of the game, the story implies that the Sacred Realm has been dealt with before.


A note on Ganon: The original Link dealt with a beast version of Ganon, who is reincarnated from game to game. The Zelda games that have Link dealing with a person named "Ganondorf" have you fighting the man who first appears in Ocarina of Time and is sealed away by the sages, only to break out of his seal in Twilight Princess.
It is my guess that this human version of Ganondorf is separate from any other "Ganondorf's" that might appear later. This means that Ganon, who appears in every single game, is probably separate from Ganondorf.
I have but a theory to support this idea: the beast version of Ganon is what the Triforce does to evil beings using it to seek power: it transforms them into Ganon. In some Zelda games, such as LttP and the original Zelda for the NES, by the time you meet the thief who took the holy power, he already has been warped by the Triforce into Ganon.

Windwaker makes a statement that directly supports this theory at the very beginning of the game, saying (paraphrased): "There was once a hero clad in green who fought back evil.... but he failed." Windwaker can't be first, but doesn't necessarily have to be last.

The worlds of both of the NES Zelda games, Zelda I and II, both feature areas in Hyrule that are drastically different than any other of the Zelda games. So, it is possible that these games occurred after Windwaker, since the flood would back up a couple of theories:
1) Without a visible Hyrule Castle in Zelda (and if I remember correctly, The Adventure of Link), these games don't necessarily have to take place in the normal "environment" that is Hyrule. (Death Mountain still exists, but maybe it takes place on the other side of the mountain, for instance)
2) Much of the land around the castle and all has been moved around, and some of the landscape has changed drastically.

The Master Sword's location can't necessarily predict the timeline of the games, but it can give hints. As far as I can tell, only in LttP and OoT do the endings of the games show that the Master Sword was returned to its pedestal. If OoT went first, followed by LttP and then by Twilight Princess, the sword's location would be accounted for in all three of the games: Stuck into its pedestal.
Following Twilight Princess, Link doesn't necessarily have to return the Master Sword into the pedestal he found it. A monument could be built somewhere else, etc. Not only that, but losing the sword could partially explain why an old man in the middle of nowhere gives you the Master Sword in the Legend of Zelda.

There are hints all throughout the games as to what order the games go in. Keep in mind that an undetermined amount of time separates the occurrence of each Zelda. Thus far, this is what the timeline looks like:

Link 1
- Ocarina of Time
- Majora's Mask

Link 2
- A Link to the Past
- Link's Awakening
- Oracle of Ages/Seasons

Link 3
- Twilight Princess

Link 4
- Windwaker

Link 5
- The Legend of Zelda
- Zelda II, the Adventure of Link

The four swords games are not included in this timeline, but I will leave the following note by Geoff Thew concerning those games themselves, as well as the lands that all of the games take place in: (some of this was edited)
"The three Four Swords games do take place in an alternate version of Hyrule... although it is possible that they only take place in the distant future. (Hence the reason I didn't add them to the timeline)
All of the [Zelda] games take place in the same world. Oracle of Seasons and Majora's Mask take place outside of Hyrule, but it is still within the same world. Windwaker takes place on "the islands", or "high above Hyrule."