The Currently Accepted Timeline
Pre-Timeline Break:
At the end of Ocarina of Time the timeline is broken up into 3 separate timelines.
The timeline where Ganondorf defeats Link during the final battle:
The timeline where Link is sent back in time by Zelda and the two stop Ganondorf before he rises to power:
The timeline where Link defeats Ganondorf but his bloodline is removed from the timeline by Zelda sending him back to the previous timeline:
The three timelines then merge into one, combining all events into one history, which leads us to the merged timeline:
I don’t really like this timeline. It’s a mess and it only gets worse with each new game which can be seen with even Nintendo keep changing with each new copy of the Hyrule Historia.
The Multiverse Theory
I will now break down these universes and explain why each game belongs in its universe.
The NES Universe:
Once Hyrule is safe, Link learns about the Legend of Zelda. The first princess Zelda was betrayed by her brother who was working with an evil wizard to try and steal the Triforce of Courage. When this original Zelda refuses to help them she was cursed with an endless sleep. Her brother, beset with guilt orders that every daughter to the royal family is to be called Zelda in her honour. After hearing this Link adventures out into Hyrule once again and collects the Triforce of courage. With this he wakes the sleeping princess from her slumber and saves the day once again.
A Link Universe:
These games are all connected by a shared map or art style.
Echoes of Wisdom sees Link and Zelda first meeting each other. Zelda is able to save Hyrule from the rifts opening everywhere. She does this with the Goddess' Prime energy which was left after they created the world.
Years pass and the Prime Energy is renamed to the Triforce. Link moves his home closer to the castle. Zelda is captured by Ganon during A Link to the Past’s opening, remembering her previous adventure she calls to Link telepathically. Link travels to the Dark World and saves Hyrule from Ganon who was after the Triforce. Ganon is killed in this conflict, much to the horror of his adopted mothers, TwinRova.
After this Link is beset by nightmares of Ganon returning once again. To try and clear his mind he sets out on a journey away from Hyrule which leads into Link’s Awakening. Link's ship is caught in a storm and he is lost at sea. He ends up trapped within the Wind Fish's dream. While in this dream he faces off with a nightmare version of Ganon.
Ready to confront his nightmares, Link returns to Hyrule where he stops TwinRova's plan to resurrect Ganon by sacrificing Zelda. The two witches instead sacrifice themselves and Ganon is resurrected as a mindless beast. Link defeats Ganon once again and peace is brought back to the Kingdom.
Decades later Hyrule is invaded by Lorule beginning A Link Between Worlds. A young boy, named after his ancestor Link, rises up and combats this new threat. He manages to use the Triforce to save not just Hyrule but Lorule too.
Years later he sets out on a journey similar to the first Link and finds the kingdom of Hytopia.
The Twilight Universe:
Hyrule undergoes a bloody civil war that sees a scared mother pled with the Great Deku Tree to give her child shelter. This child, Link, grows up with the Kokiri, a race of fairy children that never age and are protected by the Great Deku Tree.
Years later Ganondorf plans on stealing the Triforce in order to rule all of Hyrule. In order to do this he tries to enter the sacred realm but is stopped by its guardians. One of these is the Great Deku Tree, who Ganondorf poisons. Just before the Great Deku Tree dies it tells Link about Ganondorf. Link meets with Zelda who asks him to enter to sacred realm and protect the Triforce as Ganondorf attacks Hyrule. Link is able to open the path to the sacred realm but is sealed away for 7 years. During this time Ganondorf uses the opened path to the sacred to obtain the Triforce of Power. Link awakens 7 years later to find a Hyrule oppressed by Ganondorf. Link fights his way to the tyrant and is able to kill him.
Zelda feels guilty that Link lost 7 years of his childhood and so sends him back in time using the Ocarina of Time. When Link arrives in the past he informs the younger Zelda of what happened and the pair capture Ganondorf without opening the path to the sacred realm. Link then goes off in search of his fairy friend and finds the strange world of Termina. He saves this world from the evil Majora and returns to Hyrule and settles down, now known as the Hero of Time.
Ganondorf is able to break free from his bonds, forcing the sages to trap him within the Twilight realm. The Hero of Time's grandchild, Link, grows up to stop and ultimately defeat Ganondorf when he returns from the Twilight realm. He is trained by the ghost of his grandfather, The Hero's Shade, once the Hero of Time.
The Four Swords Universe:
Minish Cap > Four Swords > Four Swords Adventures
This is the universe of multiple heroes. It's connected by the Four Sword which we see created in the Minish Cap and then used in both Four Swords and Four Swords Adventures.
The Kingdom of Hyrule is attacked by Vatti who destroys the Picori Sword, unleashes monsters across the land and turns princess Zelda into stone. Link teams up with Ezlo, who sits on Link's head like a hat. The two team up with the Picori and reforge the Picori Sword, imbue it with the 4 elements turning it into the Four Sword. Link and Ezlo use the Four Sword to destroy Vatti, trapping him within the Four Sword, which saves Zelda and all of Hyrule.
A century later Link's grandson, also called Link, finds the Four Sword while adventuring with Zelda's granddaughter, also called Zelda. Vatti escapes and captures Zelda. Link uses the Four Sword to once again defeat Vatti, trapping him in the Four Sword again.
Centuries later the descendants of Link and Zelda, of course called Link and Zelda, are tricked into releasing Vatti from the Four Sword. Shadow Link captures Zelda and Link uses the Four Sword to track her down. During his adventure he learns that Vatti is in league with a new enemy. Ganon. Link fights his way to the pair and defeats them both, sealing them away within the Four Sword once and for all.
This universe contains the Light Force and Four Sword, but no Master Sword, Triforce, or secret stones.
The Flooded Universe:
These games are all direct sequels to each other which connects them into one neat universe.
Ganon rises to power and threatens all Hyrule. As no hero has risen to defeat this invasion the king of Hyrule uses the Triforce to ask the Gods for help. In a desperate last resort the Gods flood Hyrule creating a vast ocean for the few survivors. Centuries later a young boy called Link is exploring his island home when his sister is kidnapped by a giant bird. He sets out to save her with the help of a crew of pirates. Eventually he collects the scattered pieces of the Triforce and descends to the flooded land beneath the ocean. Here he confronts Ganon in order to save his sister. After a climatic battle Link kills Ganon and saves his sister.
He then joins the crew of pirates that helped him during his adventure and they set sail for a new land. Captain Tetra is captured by a ghost ship so Link sets out to save her. He learns that she was captured by Bellum and so defeats this evil spirit freeing Tetra. The crew finds a new land and found New Hyrule on its shores.
Many years later Link and Tetra's descendants team up to repair the mystical Spirit Tracks that have been damaged by an unknown force.
The Wild Universe:
The connecting factor here is Fi, the spirit within the Master Sword.
Eventually most the Zonai leave or simply die off, but one of the last Zonai, Rauru, marries a human woman, Sonia, and together they found Hyrule. Zelda from the future travels back in time and spends time with them. Together Rauru and Zelda stop Demise’s reincarnation, Ganondorf, and seal him away. Hyrule Castle is built on top of the sealed away Ganondorf in order to further trap him.
Thousands of years later Demise’s evil power escapes from Ganondorf’s sealed body and causes the Calamity, this is stopped by a mysterious hero that appears to be part human, part Zonai. Perhaps this is the descendent of Rauru and Sonia.
Many more centuries later the calamity returns and destroys most of Hyrule. Link and Zelda barely survive this calamity. Link is almost killed, while Zelda is able to contain the calamity within Hyrule Castle using her holy goddess power. A hundred years later Link awakens and sets out to save Zelda and stop the calamity once and for all. He confronts calamity Ganon, emerging the victor with Zelda's help.
A few years later the pair are investigating a strange cave that emerged under the castle. This leads them to Ganondorf's sealed body which breaks free. Zelda is sent to the past along with the broken Master Sword which leads her to met Rauru and Sonia. Fi talks to Zelda via the broken Master Sword which leads Zelda into sacrificing herself to become a dragon so that she can repair the holy weapon. Tens of, if not hundreds of thousands of years later, Link finds the Master Sword lodged within dragon Zelda's head. He removes the now repaired weapon and faces Ganondorf. After defeating Ganondorf, Zelda is returned to her human form thanks to the spirits of Rauru and Sonia.
The CD-i Universe
Years later Ganon returns again and captures Link within the land of Tolemac. Zelda sets off to save him and stop Ganon. She is successful which ends Ganon's evil in the many lands of this awful universe.
The TV Universe
Final Thoughts
Why does Link dying during the final fight Ganondorf in Ocarina of Time lead to a new timeline but it doesn't in any of the other games?
How did the timelines merge to created the world we find in the Breath of the Wild?
Why do some games had artefacts such as the Light Force, which looks like and does the same thing as the Triforce, when the Triforce also exists in these timelines?
Why does the Master Sword look different in its design in Ocarina of Time, Wind Waker, and Breath of the Wild?
How does Ganondorf keep coming back again and again and again as well as characters like TwinRova?