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Description
Right, so... This is my personal take on the timeline theory/family tree of Zelda. This is the one that's “canon” for my fanfic “Time's Wanderers.”

You read the chart like this:

A straight black line means one of two things; on the charts besides Link and Zelda's family tree, they mean the person reincarnated without being of the same lineage. On the family tree, the lines without little “z” looking breaks (i.e. straight black lines) mean there are only one or two generations between them.

The broken lines (with the little “z” things) mean many years/generations come between.

The lines that end in arrows mean the person is the same incarnation and wasn't reborn.

Hope that makes sense.

Spoiler Warning for Skyward Sword and other games in this description!

You might notice that two games are missing from the list: The original Legend of Zelda and The Adventure of Link. This is because they don't really apply to Time's Wanderers so much and/or possibly occur on a split timeline (the one where Link dies fighting Ganon in Ocarina of Time.) However, I'm not so fond of the same split timeline theories as everyone else—though I do believe in the future holding multiple possibilities. Even Wind Waker might not happen in every future; it's just one possibility. That's what I'm saying. But for simplicity's sake, I say the path of time is a bit more linear than others make it out to be. Also, I'm not 100 percent sure of where Four Swords Adventures should be placed, but I figure it'd be shortly before A Link to the Past.

Also, it's one of my personal beliefs that both Zelda and Link always reincarnate into the same linage, not just Zelda (which is the more common take on this.) Despite being joined in the beginning, their branches split off from one another early on... So the fact that I put Tetra/Zelda and Link together in Wind Waker—ages upon ages later—isn't a big deal.

Demise, Ghirahim, and Fi's charts just show their “reincarnation” paths. I don't think they come from the same line. However, I DO believe that Ghirahim and Fi's spirits reincarnate into new forms even though they're sleeping inside the weapons. Each of them constantly reincarnate as “helpers” of their respective masters... Though, as you'll eventually see, I don't think Ghirahim remains completely loyal to his master as time goes on... Though he most definitely hates the “chosen hero” with a passion.

Alright, now for the timeline theory:

Skyward Sword: Zelda and Link from Skyward Sword marry and found Hyrule and become it's first King and Queen. Demise is sealed away, but curses their families with the promise that his hatred will always come back to haunt them, thus sealing their fates to reincarnate to stop his reincarnations until the end of time.

At some point in time after Skyward Sword, there are two princes born to the royal family; one will go on to become King while the other will become a Hylian Knight in service to his brother. This is where the split in the lines begins. Zelda will reincarnate to royal line, while Link will reincarnate along the knight's line.

Minish Cap, Four Swords, and Four Swords Adventures: Ghirahim reincarnates for the first time as Vaati. Link and Zelda fight him off twice, once in the Minish Cap and again in Four Swords. (It's possible the Link and Zelda are the same incarnations both times, but the time span between Minish Cap and Four Swords isn't completely clear I favor the theory that they are indeed the same incarnations.) In any case, Vaati is defeated and sealed away.

Years pass and new incarnations of Link and Zelda fall victim to the tricks of Vaati and Ganon (the first incarnation of Demise's hatred) tries to break free by using Shadow Links and the Dark Mirror that will later go on to become the Mirror of Twilight beyond which the Twili live. Vaati is sealed away for a third and final time, and Ganon is defeated along with him.

A Link the the Past, Oracle Series, and Link's Awakening: By the time of A Link to the Past, the knight's line is dying out. This Link, in fact, is the last of his line after the death of his uncle. He rises to save Zelda and fights against a reincarnation of Ganon and Ghirahim's new incarnation, Aghanim. After saving Hyrule, he sails off to train and takes a role in the Oracle Series before sailing back and getting stranded on the island where Link's Awakening takes place.

After returning to Hyrule, he settles down and starts a family, and the line continues.

Ocarina of Time/Majora's Mask: In the time of the brutal Hylian Wars, many people are killed. Notably, the line of the knight and the Sheikah are all but wiped out. Impa, the current Zelda's nursemaid, has a son of the same age as Zelda named Sheik—whose name and appearance Impa will eventually let Zelda borrow for the seven years of darkness while her son, the real Sheik, is hidden away in the Sacred Realm where the evil can't harm him.
The last child born to the knight's line, a woman named Arina, marries the knight Lance and gets with child not long before he is sent away to the front lines. He is captured and presumably killed, and Arina is forced to flee their home under attack. She is wounded outside the Forest of Legend but manages to reach the heart of the forest.
She meets a young Kokiri girl named Saria, who helps her give birth to her son before she dies. The boy becomes the new incarnation of Link and is, once again, the last of his lineage. He becomes the Hero of Time. After defeating Ganondorf with the Sages and Zelda, he leaves and goes to Termina where he remains for a long, long time reliving the same three days over and over. When he finally returns to Hyrule...

Link discovers that at least a century has passed in his homeland. Much has changed, and the Hero of Time rides off into the forest on Epona in search of somewhere to stay. He discovers the town of Ordon, where he settles.

Twilight Princess: Years pass, and eventually this Link is called to defeat Ganon once again with the help of a different Zelda. The adventures of Twilight Princess take place, Link discovers his wolf form and meets the Spirit Wolf/Spirit Knight (who, unknown to Link, is actually his father Lance.)

After Twilight Princess, Link is granted the title “Hero of the Twilight” along with the title “Hero of Time,” though most people do not realize that this Link is the hero of that legend as well.

The adventures of Time's Wanderers take place shortly after Twilight Princess.

Link eventually marries Saria and his line continues into the distant future...

Wind Waker, Phantom Hourglass, and Spirit Tracks: Ages pass and Ganon breaks free from his prison once again. This time, for some reason, no hero rises to defeat him and the gods are forced to flood Hyrule. As time goes on, the legends of the heroes of old survive on the wind's breath and eventually Link and Zelda reincarnate once again. The adventures of Wind Waker take place, during which Ganon is (presumably) sealed away for the final time.

In Phantom Hourglass, Link and Tetra/Zelda go searching for new lands to settle and meet up with Bellum, who is Ghirahim's new incarnation. He is defeated yet again by the Hero of Winds.

Link and Tetra/Zelda finally find a new continent sometime after Phantom Hourglass and found a new Hyrule.

About a century later, they both reincarnate once again; Zelda as their grandchild and Link as Aryll's grandson. Demise's hatred reincarnates in a new form, the Demon King Malladus. Ghirahim's spirit reincarnates in part as Byrne... Who, during the events of Spirit Tracks, is wronged by Malladus. He sides with Link and Zelda and helps them defeat his master. In doing so, ends up destroyed by Malladus. The next time he returns, he will have no memory of his past life.

Thus, Malladus is defeated and peace returns to Hyrule once again.

And time passes on, ever into the future...

.
Edit: I have tweaked a few things since making this, if anyone still looks at it and reads all this. The main thing is that it's entirely possible that the Fairy Queen of Wind Waker is actually Navi - and Ceila and the other fairys that help Link in Phantom Hourglass are her children of sorts. And since I know my idea about OOT Link and TP Link being the same person is only part of Time's Wanderers, I still think the rule of reincarnation applies - Ghirahim reincarnates as Zant and Fi as Midna. I'm still curious to see how future games can be worked into my theory, and whether or not I can work in the rest somehow.

Description
Right, so... This is my personal take on the timeline theory/family tree of Zelda. This is the one that's “canon” for my fanfic “Time's Wanderers.”

You read the chart like this:

A straight black line means one of two things; on the charts besides Link and Zelda's family tree, they mean the person reincarnated without being of the same lineage. On the family tree, the lines without little “z” looking breaks (i.e. straight black lines) mean there are only one or two generations between them.

The broken lines (with the little “z” things) mean many years/generations come between.

The lines that end in arrows mean the person is the same incarnation and wasn't reborn.

Hope that makes sense.

Spoiler Warning for Skyward Sword and other games in this description!

You might notice that two games are missing from the list: The original Legend of Zelda and The Adventure of Link. This is because they don't really apply to Time's Wanderers so much and/or possibly occur on a split timeline (the one where Link dies fighting Ganon in Ocarina of Time.) However, I'm not so fond of the same split timeline theories as everyone else—though I do believe in the future holding multiple possibilities. Even Wind Waker might not happen in every future; it's just one possibility. That's what I'm saying. But for simplicity's sake, I say the path of time is a bit more linear than others make it out to be. Also, I'm not 100 percent sure of where Four Swords Adventures should be placed, but I figure it'd be shortly before A Link to the Past.

Also, it's one of my personal beliefs that both Zelda and Link always reincarnate into the same linage, not just Zelda (which is the more common take on this.) Despite being joined in the beginning, their branches split off from one another early on... So the fact that I put Tetra/Zelda and Link together in Wind Waker—ages upon ages later—isn't a big deal.

Demise, Ghirahim, and Fi's charts just show their “reincarnation” paths. I don't think they come from the same line. However, I DO believe that Ghirahim and Fi's spirits reincarnate into new forms even though they're sleeping inside the weapons. Each of them constantly reincarnate as “helpers” of their respective masters... Though, as you'll eventually see, I don't think Ghirahim remains completely loyal to his master as time goes on... Though he most definitely hates the “chosen hero” with a passion.

Alright, now for the timeline theory:

Skyward Sword: Zelda and Link from Skyward Sword marry and found Hyrule and become it's first King and Queen. Demise is sealed away, but curses their families with the promise that his hatred will always come back to haunt them, thus sealing their fates to reincarnate to stop his reincarnations until the end of time.

At some point in time after Skyward Sword, there are two princes born to the royal family; one will go on to become King while the other will become a Hylian Knight in service to his brother. This is where the split in the lines begins. Zelda will reincarnate to royal line, while Link will reincarnate along the knight's line.

Minish Cap, Four Swords, and Four Swords Adventures: Ghirahim reincarnates for the first time as Vaati. Link and Zelda fight him off twice, once in the Minish Cap and again in Four Swords. (It's possible the Link and Zelda are the same incarnations both times, but the time span between Minish Cap and Four Swords isn't completely clear I favor the theory that they are indeed the same incarnations.) In any case, Vaati is defeated and sealed away.

Years pass and new incarnations of Link and Zelda fall victim to the tricks of Vaati and Ganon (the first incarnation of Demise's hatred) tries to break free by using Shadow Links and the Dark Mirror that will later go on to become the Mirror of Twilight beyond which the Twili live. Vaati is sealed away for a third and final time, and Ganon is defeated along with him.

A Link the the Past, Oracle Series, and Link's Awakening: By the time of A Link to the Past, the knight's line is dying out. This Link, in fact, is the last of his line after the death of his uncle. He rises to save Zelda and fights against a reincarnation of Ganon and Ghirahim's new incarnation, Aghanim. After saving Hyrule, he sails off to train and takes a role in the Oracle Series before sailing back and getting stranded on the island where Link's Awakening takes place.

After returning to Hyrule, he settles down and starts a family, and the line continues.

Ocarina of Time/Majora's Mask: In the time of the brutal Hylian Wars, many people are killed. Notably, the line of the knight and the Sheikah are all but wiped out. Impa, the current Zelda's nursemaid, has a son of the same age as Zelda named Sheik—whose name and appearance Impa will eventually let Zelda borrow for the seven years of darkness while her son, the real Sheik, is hidden away in the Sacred Realm where the evil can't harm him.
The last child born to the knight's line, a woman named Arina, marries the knight Lance and gets with child not long before he is sent away to the front lines. He is captured and presumably killed, and Arina is forced to flee their home under attack. She is wounded outside the Forest of Legend but manages to reach the heart of the forest.
She meets a young Kokiri girl named Saria, who helps her give birth to her son before she dies. The boy becomes the new incarnation of Link and is, once again, the last of his lineage. He becomes the Hero of Time. After defeating Ganondorf with the Sages and Zelda, he leaves and goes to Termina where he remains for a long, long time reliving the same three days over and over. When he finally returns to Hyrule...

Link discovers that at least a century has passed in his homeland. Much has changed, and the Hero of Time rides off into the forest on Epona in search of somewhere to stay. He discovers the town of Ordon, where he settles.

Twilight Princess: Years pass, and eventually this Link is called to defeat Ganon once again with the help of a different Zelda. The adventures of Twilight Princess take place, Link discovers his wolf form and meets the Spirit Wolf/Spirit Knight (who, unknown to Link, is actually his father Lance.)

After Twilight Princess, Link is granted the title “Hero of the Twilight” along with the title “Hero of Time,” though most people do not realize that this Link is the hero of that legend as well.

The adventures of Time's Wanderers take place shortly after Twilight Princess.

Link eventually marries Saria and his line continues into the distant future...

Wind Waker, Phantom Hourglass, and Spirit Tracks: Ages pass and Ganon breaks free from his prison once again. This time, for some reason, no hero rises to defeat him and the gods are forced to flood Hyrule. As time goes on, the legends of the heroes of old survive on the wind's breath and eventually Link and Zelda reincarnate once again. The adventures of Wind Waker take place, during which Ganon is (presumably) sealed away for the final time.

In Phantom Hourglass, Link and Tetra/Zelda go searching for new lands to settle and meet up with Bellum, who is Ghirahim's new incarnation. He is defeated yet again by the Hero of Winds.

Link and Tetra/Zelda finally find a new continent sometime after Phantom Hourglass and found a new Hyrule.

About a century later, they both reincarnate once again; Zelda as their grandchild and Link as Aryll's grandson. Demise's hatred reincarnates in a new form, the Demon King Malladus. Ghirahim's spirit reincarnates in part as Byrne... Who, during the events of Spirit Tracks, is wronged by Malladus. He sides with Link and Zelda and helps them defeat his master. In doing so, ends up destroyed by Malladus. The next time he returns, he will have no memory of his past life.

Thus, Malladus is defeated and peace returns to Hyrule once again.

And time passes on, ever into the future...

.
Edit: I have tweaked a few things since making this, if anyone still looks at it and reads all this. The main thing is that it's entirely possible that the Fairy Queen of Wind Waker is actually Navi - and Ceila and the other fairys that help Link in Phantom Hourglass are her children of sorts. And since I know my idea about OOT Link and TP Link being the same person is only part of Time's Wanderers, I still think the rule of reincarnation applies - Ghirahim reincarnates as Zant and Fi as Midna. I'm still curious to see how future games can be worked into my theory, and whether or not I can work in the rest somehow.