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Um, I believe it is up in the air. Only definite facts are OoT is 1st so far, MM and WW are the two beginning on each split (confirmed in an interview), TP is on the MM side was confirmed by Shigure Miyamoto (I'll get the interview in a few hours or so), LA is after ALttP, OoA/OoS are around the same time but have no particular order that matters, MC is before FS which is before FSA, and the first LoZ is before AoL.

OoT was originally a prequel to ALttP directly, but that plan was changed when Miyamoto said in an interview that WW is exactly 100 years after Adult Princess Zelda sends Link back in time. Link in the paradox goes on to the events of MM, but he no longer exists in the time line with Adult Zelda and the Sages sealing Ganon away. ALttP is now canonically referring to another war that lasted 7 years in which lore refers to the Knights of Hyrule as opposed to just one Hero like most stories with reference to a past Link. However, what exactly happens to Ganondorf is never explained in that side of the timeline after Link is in the past. Links does have enough knowledge of Ganondorf's plans to possibly start a prosecution process and have legal actions taken against him.

OoA and OoS aren't directly related to a particular Link but the fact that Twinrova are still alive points to the MM timeline. This is because they clearly die when defeated by Adult Link and the time paradox prevents those events from happening when Link grows older without taking the Master Sword. Because the fate of Ganondorf is still unknown in the MM timeline after OoT, it's safe to assume one of the games in the timeline leads to him becoming Beast Ganon and getting defeated by another Link before these games occur.

In Twilight Princess, Ganon has escaped a Prison he was sent to years ago. Originally this story was going to have the same Link from OoT after he'd grown up. This would've meant that Ganon's imprisonment was a direct consequence of his misdeeds in OoT. This could still be true and probably is, as he obtained the Triforce of Power spontaneously. This can be explained by the time paradox, as Link has the Triforce of Courage when he is sent back in OoT and the paradox would create two Triforces of Courage in one timeline and zero on the other if one hadn't stayed with Adult Zelda and the other took it's place in Link's possession. However, the obtaining of one Triforce leads the others to seek out the appropriate owners mainly Zelda and Ganon. It is possible that the Link who grew up in Ordon is a descendant of the OoT Link (The ranch job points to Link and Malon hooking up but that is speculation). Ordon Link already owns the Triforce of Courage even if he doesn't know it, and it protects him from the effects of the Twilight spreading over Hyrule to an extent. Zelda already has the Triforce of Wisdom in the opening sequence as Zant invades Hyrule Castle.

Wind Waker is as stated 100 years after OoT on the side Link got sent back in time and ceased to exist. Some games have stated a Link is a descendant of the original and that would be impossible in this situation. The Link in this timeline lives in a flooded Hyrule and legend says the Hero traveled through time furthering the argument of the story being in the timeline Link disappeared from. Games after WW would have to take place long enough after for tectonic activity to lift Hyrule above sea level of for the flood waters to recede. Other than this, geography of Hyrule shouldn't be used as a source of reference being that Kakariko Village, Lake Hylia, Death Mountain and other various landmarks change location very frequently and other landmarks such as the Minish Woods appear only in games that they're important in. PH is directly after WW.

MC has the most geographical confusion of all the games as several key landmarks cease to exist and new ones pop up. Because it's possible that these areas have had their names changed over centuries of slang and property ownership or that Link has no reason to trek the long distances to various locations that were in other games there is no reason to believe that the geography has anything to do with the timeline. After all, the Picori who hid the 4 Elements are very small and couldn't travel great distances frequently. Because the Four Sword is forged from the remains of the Picori Sword it's safe to say that this story is before FS and FSA. Though it's unclear whether Link in FS and Link in FSA are the same Link, it's more probable that FS came before FSA as Vaati is killed at the end of FSA instead of sealed. There is a possibility that another Link was involved in the story of the Picori Sword and the "Force" made by the Picori to originally seal monsters away, but no game has been made with that story (yet). No evidence in these games suggests any timeline, which is why the parallel timeline theory, meaning MC, FS and FSA had nothing to do with either the MM or WW timelines, came about. However, similarly to ALttP items like the Moon's Pearl and Dark Mirror exist. It seems from talk with the Gerudos that Ganondorf may have been reborn after a previous death or that history repeats itself (exactly down to the name) as Ganondorf was being worshiped by Deku Scrubs in the Lost Woods, and had entered a forbidden Pyramid leading him to be excommunicated by the Gerudo society.

ALttP was originally in the place of WW but is now in a foggy category. LA comes directly after it, and neither seem to bear any resemblance to a specific side of the time line. The only facts are that MC, FS, And FSA have similar artifacts and may be related with further effort. The only clue is that Link has a bloodline related to former Knights of Hyrule possibly Link from another game. Because not enough evidence is presented in this case I would put it in the MM side because of a hunch of mine regarding the Dark mirror, Dark Realm, Trident of power in FSA (which is linked in one way to ALttP via the Moon Pearl) being similar to the Spear Midna uses when controlling the fused shadows, and the Twili Tribe and Zuna Tribe having a similar past (same tribe maybe?).

The original LoZ could be almost anywhere at first glance but the connections in AoL are more reliable. Because several towns are named after sages from OoT (though technically the sages were named after the towns) who became famous from the hero of time legend it appears to be on the WW side of the time line (there were glass mosaics of the sages in the chamber the Master Sword was being held in during WW).

holy wow!!, lots of re-search i like 3nodding

but........its zelda...........why do we have to worry on time lines?......cores we want Zelda to go on with out the burden of explaining stuff?
(just mi thou)

cuzz i rily just dont no where the time line thing is going......i gave up after Loz~WW lolo...it just got to confusing for mi O.o O.o o.o

but agein, just mi................lolollolololo

cuzz if ya guys can explain that time line thing that will be even better xd