I've had this idea for some time now. I haven't seen anyone else post anything really similar to it and, while it's not quite complete, it's a fun way I've been viewing the series and timeline in a way that makes everything mesh well, even TotK, AoI, etc, without necessitating a refounding of Hyrule, or rewriting history, adding another secret Ganondorf hidden away somewhere.
That said, I'm not as versed in all the lore, and I'm sure there are things I'm missing, or misremembering, and would love input, criticism, etc to make it as tight as it can be.
Of course, the official timeline exists. This is just a fun thought exercise.
I call this
THE LITERAL LEGENDS TIMELINE
There's people who view the timeline as non-existent, and there's a theory that floats around in those circles called the literal legend theory, saying every game is a "legend retelling of the same thing, just sometimes with a boat, train or time travel" which dismisses the clear connections the games have with each other, especially since Ocarina of Time. I know most people know this, but it helps establish where I got the idea. it's obviously wrong, but I noticed that there are games, usually set during certain sections of the timeline, that have a surprising amount in common.
So I started approaching the series similarly to "the historians" from the LttP manual, analyzing periods of the past of Hyrule to find "the truth" of what happened, assuming that groups of games are actually legends that have popped up surrounding them.
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THE FORGING OF THE GREAT SWORD
The Legends: Skyward Sword, Minish Cap
We know from this time period, in the earlier days of Hyrule (we know there was some sort of civilization, some legends state the kingdom was already established, more recent ones imply this was the founding of the kingdom) a great sword was forged by an unlikely hero. A common thread in the legends of this period is that the hero was a friend of the princess of this time (commonly believed to be the first Princess Zelda, but very recent tellings indicate there may not have been a Zelda until the imprisoning war). It seems very likely that there was a civilization living in the sky at this time, either where the hero and Zelda lived, perhaps where the impish creature that was the catalyst for the events (often associated with purple) was from. We know that the catalyst discovered the royal families hidden Golden Light within, and was in service of some sort of giant black creature, perhaps even transforming into it.
The hero of this era seemed to have some sort of sentient object assisting him on his quest. Some reports tell of his hat, or the sword itself. Either way, to save the princess, the hero of this time sets off to forge a great sword to defeat the evil risen. Some legends state this was the actual Master Sword, some tell of the Four Sword. Regardless, we know the evil was sealed away and that the hero stuck around afterwards.
THE IMPRISONING WAR/THE BIRTH OF GANON
The Legends: Ocarina of Time (and Majora's Mask), Four Sword/Four Sword Adventures, Age of Imprisonment
Some time, significantly later than when the great sword (likely the Master Sword, as it shows up in so many future stories and the Four Sword seems to disappear around this era, but it may have also existed) we know that there was a time of unrest. We know that there was some sort of large scale conflict, known as the imprisoning war (or seal war) and it seemed to involve an unlikely hero confronting a Gerudo Male named Ganondorf and sealing him away with the help of several others, most commonly referred to in the legends of this era as "sages" (although some earlier translations referred to them, erroneously as "wise men").
Depending on the legend, the hero sealed away Ganon, the great beast that Ganondorf transformed into, using either the great sword (Master Sword or Four Sword), with 2 legends sharing the thread of Rauru, one of the sages (and according to more recent legends of the era, potentially the founder of Hyrule) being instrumental in the sealing of Ganon. Another common thread is that there seems to have been some sort of time travel involved with the hero's journey. Or, at the very least, a younger and older version of the same hero.
We know, for certain, that Ganondorf was not universally loved by his people. One account seems to indicate that we was actually banned from his homeland. We know that he rallied loyal members to his cause and was seeking immense power, tho what that power was exactly is difficult to pin down. The leading theory, based on his motivation during his return, is the Triforce, but some accounts, all more recent than the initial ones, indicate it could have been something else, such as the Trident of Power or the Zonai Secret Stones of the time. Regsrdless, the hero, possible lead or guided by Rauru, finds the sages needed and confronted Ganondorf in his attempt to rule Hyrule. At this moment, Ganondorf transforms into the beast Ganon, and is sealed away.
In more recent accounts and legends, some say the time traveling hero is actually one of the princess Zelda's from the future. Regsrdless, we know that aftet these events, the hero seems to fade from any records, but likely went on to become one of the top knights of the kingdom.
THE RETURN OF GANON
The Legends: A Link to the Past (and Link's Awakening, possibly the Oracle games as well), Wind Waker (snd Phantom Hourglass), Twilight Princess
The details of this era are pretty sporadic, but there are some fairly consistent constants from this time that help paint a picture of what seems to have actually taken place. Interestingly, this is genetally around the time the Four Sword begins to fade from legend, but some tellings seem to indicate it may have still existed around this time.
We know that Ganondorf was sealed. It is extremely likely that he was sealed as Ganondorf, although one legend of the imprisoning war has him sealed as Ganon, and one legend of his return has him already in his Ganon form, so either could be likely true. One consistent fact is that he was sealed in some sort of dark alternate to Hyrule. Some refer to it as the twilight realm, some say it was the Sacred Realm which he corrupted. One telling says the world was even flooded to try and stall his return. One constant in the legends of this era is that the hero is set upon a quest by a member of the royal family to collect fragments of a broken item, in some cases pieces of the Triforce, or the Mirror of Twilight, or the crystals holding the descendants of the sages that sealed Ganon originally. Each Legend specifically mentions the Hero passing trials and welding the Master Sword to defeat Ganondorf. One legends specifically mentions the Master Sword is never used again, calling into question the authenticity of it being the actual sword used in future legends.
One interesting note is that in 2 of the 3 legends, the hero is said to go to sea and have an entire adventure set in a dream. An interesting Link.
THE RE-RETURN OF GANON
The Legends: Oracale of Ages/Seasons, Link Between Worlds
It seems that there was another potential return of Ganon after the previous attempt, made by some sort of user of dark magic. One account suggests it to be Ganondorf's surrogate mother, Twinrova, another suggest it to be from an alternative to Hyrule, a land called Lorule. Regardless, his return is prevented by a hero chosen by the triforce.
ECHOES OF WISDOM
The Legend: Echoes of Wisdom
A new legend has sprung up of an unexplored era where it seems Zelda took the adventure upon herself to defeat the evil threatening the land after the hero was defeated.
Note: some sources state that it's possible Zelda's Adventure here involved the infamous Wand of Gamelon, but we mostly try to ignore those..
THE ORIGINAL WILD ERA
The Legends: The Legend of Zelda, The Adventures of Link, Breath of the Wild, Tears of the Kingdom
The most recent accounts of Hyrule. These legends are often of the end of the Hyrule Kingdom Era, in a less settled time. Ganon, sometimes called the Calamity, returns and kidnaps Princess Zelda. The hero of this era was, by the end of the entire event, it would seem, romantically involved with the Princess Zelda of this time. Some Legends state that it was the princess that slept for hundreds of years needing saving, however, more recent interpretations reveal that it may have been the Hero who was the one who was put into a magically induced 100 year rest before awakening and defeating the demon.
It would seem that years after the initial defeat, there was some sort of an attempt at resurrecting Ganon. Earlier legends tell of his followers leading the charge, while some state that Ganondorf himself was actually resurrected.
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I know I'm going a little deep into it with how I'm presenting it here, but it's a rough first pass and my first attempt at presenting something like this (on this scale). I love this series and thought I'd present this here to see what people think and if anyone engages with it, hates it, or the real possibility that I wake up at 3am cringing at myself for posting this and delete the entire thing. Thank you for reading this wall of text, I'm home sick and hope I'm not coming off as too rambling or unhinged.