Going by my own current timeline, this is how I belive the life of Ganondorf happens:
Adult Timeline: Ganondorf born (Pre-
OoT), manipulates the King of Hyrule, takes over for seven years, becomes pig Ganon, sealed in the Sacred Realm by the Awakened Sages (
OoT - adult ending), escapes the Sacred Realm by reasons unknown, attempts to rule Hyrule, Great Flood happens (post-
OoT, Pre
tWW), events of The Wind Waker happen, Ganon killed and Master Sword lost (
tWW), based on common theroy, Ganon's spirit comes back during the early era of the new Hyrule, dostroyed by Link (
LoZ), his minions attempt to revive him using Link blood and fail epicly (
AoL), minions continue to attempt to revive Ganon, Twinrova truly does come back for revenge, Ganon's spirit sealed within the Trident (
OoA/
OoS), Ganon is absent (
tMC,
FS), Ganon reincarnated in new Gerudo male who touches the Trident that he is sealed within during the Oracles and uses Vaati, unforunate for him, the Master Sword may be gone, but there is the Four Sword now instead, in which he is sealed(
FSA)
Child timeline: Ganondorf born (pre-Ocarina of Time), after Link is sent back in time with knowledge of Ganondorf's planned invasion, Link and Zelda let him be, until he does 'something outrageous' - theorizing to be destoyed the Temple of Time - and is executed by the Sages, realizes he has the Trifroce of Power, the Sages fail... epicly, sent to the Twilight Realm (post-
OoT/
MM, pre-
TP), manipulates Zant and hosts his power within him, spreads Twilight over Hyrule, events of Twilight Princess happen, transforms into beast GANON, fights Link, loses Trifroce of Power, killed by Link (
TP), Potent has absolutely no idea how Ganon comes back for
aLttP, he theorizes that the Triforce was unifed following
TP, Ganon destroys Nerushi for not agreeing with Potent, it turns out that Potent reived Ganon at some point to support his timeline, the events of
aLttP happen, Ganon uses Agahnim in a very similar manner to Zant and posses him in s similar way to possesing Zelda in
TP, creates the Dark World, eventually killed by Link and destroyed for good by Silver Arrows (
aLttP)
I'm aware of the strong connection between Twilight Princess and A Link to the Past, but I have no idea how he came back. But I go by the fact that Twilight Princess is strongly connected to A Link to the Past. Because I don't know how he came back, I had to made an obsurd theory inbetween involving one of my fellow theorists who is the reason I put A Link to the Past on the child timeline, and I am sour for giving in. >_>
Small fan theroy: River Zora is the reason there are no Zoras left in A Link to the Past- he kicked them all out of the domain because he can.
