Edited 21-3-2015
Of Gods:
Ganon
I've mentioned that I think Ganon does not equal Ganondorf, and this is why...
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Ganon
The Boar God of Chaos, King of Darkness, and Dark Lord, Ganon is an aspect/avatar of Mawt who frequently breaks into the gods' realms, causing death and destruction. He often uses pawns to help him re-enter Hyrule.
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Okay, so first, the history of Ganon and Ganondorf, as crib noted from canon.
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ADULT: _1; SS; _2; MC; [FS; FSa;] OoT; ALttP; ALBW; [LoZ; ZII]
FSa –
Ganondorf the nomad (no longer Gerudo due to lawbreaking) is mentioned, and though he does not appear he is reported to hare off into the desert after some item of power releasing Ganon. Ganon is sealed in the Four Sword (recently vacated by the now vanquished Vaati.)
OoT –
Ganondorf sneaks into the Sacred Realm to try and steal the Triforce. He touches it creating the Dark Realm but can only keep Power. At some point (then or later is uncertain) he become able to change his form to a boar-like creature, Ganon. Ganon (-dorf) is banished to the dark realm by the Hero and Sages.
ALttP –
The back story says Ganondorf was the first to enter the sacred realm, killed his minions and touched the Triforce, turning the Sacred Realm Dark and him into a boar (debatably a demon or god). He was locked away by the sages. Basically Ocarina of Time. Ganon eventually a, creates an avatar (indicating god hood) or b, gains a follower (god or demon) the wizard Agahnim and escapes. Agahnim is eventually killed and Ganon rises from his body. Ganon is killed.
LoZ and ZII –
The back story again says Ganon was once a man, now boar. He either regained or never lost the Triforce of Power, and appears as Ganon. He is killed. (And resurrected as Ganon if ZII is lost).
CHILD:_1; SS; _2; MC; [FS; FSa;] [OoT; MM;] ([OoS; OoA;]) TP
FSa –
Ganondorf the nomad (no longer Gerudo due to lawbreaking) is mentioned, and though he does not appear he is reported to hare off into the desert after some item of power releasing Ganon. Ganon is sealed in the Four Sword (recently vacated by the now vanquished Vaati.)
OoT –
Post adult adventure Ganondorf is mad rather than the calculating bastard from the adult time line. Why? Unknown. This information is from TP back-story. Ganondorf is banished.
OoA and OoS –
When the flames of Destruction, Despair and Sorrow were lit, Ganon the mindless, destructive boar demon god was summoned. Ganon killed.
TP –
Ganondorf (formerly banished and now considerably saner seeming) tricks a Twili (his follower) into helping him back into Hyrule. He turns into the Mad Boar. Ganon is overcome by Midna (off-screen), either banished or dead. Ganondorf remains to overcome Midna. Ganondorf is killed.
DOOMED: (_3;) [WW; PH;] ST
TWW –
Ganondorf the man reappears – there is a boar puppet, but he himself does not become one, or show any of the Boar's traits. He's just a cold (and regretful) man who thinks he's finally had his day. Ganondorf is killed.
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K! So let's make a history.
Because people rarely name their children after world destroying evil doers, FSa and OoT Ganondorf are the same man – probably a teen or twenty-something who got himself banished for thinking with the wrong head and doing something stupid and illegal and then a forty-something who had won back his people, become king and was 'negotiating' with the High King of Hyrule at the time of his coup.
Ganon, a god and aspect of the greater Chaos god, had at some point broken into the world. It may be that the young Ganondorf brokered a deal for his passage as a namesake of the God and ready-made acolyte. (This probably involved the saving or sparing of his people somewhere in the deal.) In any case the god came, created the Shadow of the Brightest Light and freed Vaati, now a demon from powers given by Ganon and stolen from the Four Sword, loose. Ganon was quickly sealed into the Four Sword by a Hero but might maintain tenuous ties to Ganondorf.
A war broke out between Hyrule and her neighbours. Ganondorf was allowed back into the Gerudo and regained enough esteem to become the Gerudo King. By the time the war ended and the King of Hyrule was now the High King. Ganondorf negotiated with the King, and as the Gerudo's sacred relic for safe keeping may have received the Four Sword. [Re: Spiritual Stones gifted by the King. The other tribes negotiated for similar terms.] Otherwise he may have been somehow bound to Ganon in the events of FSa. (Names are important - if you barter with demons don't be their namesake ~ a PSA.)
Once the Sword was in his possession, Ganondorf 'joined' with his god, or strengthened bonds becoming partially possessed in exchange for power, and staged his coup on the High King, wiping out all but the Princess from that royal family. (If you haven't read 'Magic' there's several royal lines in this universe. Also, if he was still bound after FSa the Sword is unnecessary - maybe the negotiations were going poorly and he decided to just go for it.) Since he was unable to attain the Spiritual Stones on his own he could either see if the Kid opened the Door of Time, or now he could break in with his god's backing. Since the Kid did it, he didn't need to break open the Door – a fortunate thing since that would have caused a permanent breach. Hard to seal things you can't shut.
When the Hero of Time eventually overcomes the partly possessed Ganondorf, Ganondorf cedes completely to (or perhaps can no longer hold off) Ganon, in whose control they take the form of the Boar God. Ganondorf/Ganon are defeated (not killed) and sealed in the Dark World.
In the Dark World Ganon relinquishes control of Ganondorf but keeps him as a servant – now an immortal one, as he has the Triforce of Power and Ganon's influence.*
*Note: Immortals don't die of old age – but they can die. They are also at least partially divine, and thus can only be killed by divine means.
Time forks. Three things remain constant: the Triforce bearers, their state of mortality, and Ganondorf no longer being possessed.
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Child Timeline
The old Sages act – but the one they need to seal is no longer there, something they fail to realise. They capture Ganondorf, driven mad by the sudden tearing from his god that occurred when time turned back, but still immortal and a Triforce bearer. He kills two Sages before they banish him through the Mirror of Twilight, which has not been used in many ages. (The Sacred and/or Dark realm was not an option at this point - possibly doesn't exist.)
After returning from Terminia, the Hero of Time, still the bearer of courage, travels to neighbouring Labrynna and Holodrum to counter other agents of Chaos and followers of Ganon - including Twinrova who want to raise their son/god - who succeed in summoning the mad god. The Hero kills the incarnation of the god.
Ganon's spirit drifts and eventually comes back to his partly recovered (but now bloodthirsty) servant Ganondorf who is recovering and quietly living in the Twilight Realm. Reunited Ganondorf uses the power and direction offered to ensnare a mad and greedy Twili, Zant, and makes him an acolyte, immortal so long as he has a living connection to Ganon. Zant stages a coup against his world's leaders and opens the way back into Hyrule, pulling Ganon(-dorf) across the worlds with him.
Zant is defeated by a new Hero, the Sacred Beast, who is now the bearer of Courage. The Sacred Beast destroys the Boar's physical form, and the Twilight Queen conquers its spirit to save the Princess and Hero - but falls to Ganondorf. The Sacred Beast kills Ganondorf who the Triforce of Power abandons.
Ganondorf is dead and gone – forever – but Ganon will eventually find a way back. He always does.
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Adult Timeline
Ganon and Ganondorf, now separate, are banished in the Dark World after crossing the Hero of Time and the Sages. Ganondorf's sanity at this point is debated, but he gives the Triforce of Power to his god.
Years pass by and the seal grows weak. Ganon is eventually able to create an avatar, the Sorcerer Agahnim. Agahnim grows in power, entering first the king's council, and then begins supplanting the king. He uses his powers to find the descendants of the Sages who sealed him, and use them to reverse the seal completely. He succeeds but is pursued into the Dark World by a new Hero. Agahnim's defeat at the hands of the Hero releases Ganon's true form. The Hero kills him and claims the full Triforce and uses it to restore the land. Eventually something causes the Triforce to redivide again, Power returning to Ganondorf, Courage to await another Hero, and Wisdom to the keeping of the Royal families.
An age passes. Ganon takes the Triforce of Power from Ganondorf and escapes the Dark World, leading an army against a much changed Hyrule, only to be killed by a Hero who isn't even Hyrulian. The Hero claims Power from him, already possesses Wisdom, and in the process of dealing with Ganon's worst underlings earns the whole Triforce in trial by fire. He uses it to free an ancient princess.
The Triforce divides again, Power to Ganondorf, Wisdom to the crown, and Courage to lie in wait.
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Doomed
After any game after OoT in either timeline:
Ganon escapes and incarnates again, leaving Power to Ganondorf who escapes quietly in his wake. The Hero either fails or does not appear at all, so at the pleading of the people the Gods seal Hyrule with water rather than have it fall under Chaos. Ganon is defeated but Ganondorf is free – if limited by the still present ancient seal on his power.
Ganondorf eventually becomes a relevant political/renegade power on the seas to ease his search for the rest of the Triforce, which he aims to use to restore Hyrule to its glory. (Under his and his people's rule, of course.) He is at this time unaffiliated with Ganon, who he long since saw the truth of. He is opposed by the descendant of the last Royal house and the Hero of Wind. He uses them to form the Triforce, but the last High King of Hyrule gets the wish: to permanently bury Hyrule – his enemy her – and for a new country to be founded.
The Triforce vanishes entirely.
Ganondorf, now mortal, is killed by the Hero of Winds.
Ganon remains buried in the ruins of the old world.
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Does thus end the Boar? May Hyrule never need know.
