The most talked about and also the most confusing, in my opinion, Legend of Zelda lore point is the timeline. I think that when people who haven’t looked into Legend of Zelda lore either at all or not that much can be easily confused by the timeline and how it’s laid out. The main reason for that I think is the fact that the timeline doesn’t go by the release order of the games. Instead it focuses on the story of each game and places them in order. I’m going to start off by just listing the order of the games and then go back and do like full lore. This might not hold up very well throughout time because of the fact it can so easily be changed by the Legend of Zelda community, but currently this is the order and lore behind the timeline. 

Order of games

The first game in the timeline is Skyward Sword, then The Minish Cap, after that is Four Swords, and then Ocarina of Time. This is where the timeline gets a little weird and splits. This is because of the time travel that occurs in Ocarina of Time. The Timeline splits into the child and Adult timeline and a separate ‘What if?’ type situation where the hero (Link) dies. Down the child timeline first we have Majora’s Mask, the direct sequel to Ocarina of Time. After that is Twilight Princess and then Four Swords Adventure (Yes it is a different game from just Four Swords, I’m not sure why Nintendo decided to name them so closely). In the adult timeline first you have The Wind Waker, then its direct sequel Phantom Hourglass, and after that is Spirit Tracks. In the ‘What if?’ timeline, otherwise known as the downfall timeline the first game is A Link to the Past, then Oracle of Seasons and Oracle of Ages, then Link’s Awakening, then The Legend of Zelda (the original game) and finally Adventure of Link. We aren’t really sure where Breath of the Wild, the most recent Legend of Zelda game, fits in the timeline but most think it's where the timeline reconnects.

Lore

Before the Split

The timeline, lore wise, actually starts before the first game. It starts with the Heavens and Earth being created by The Golden Goddesses, Din the goddess of Power, Nayru the goddess of Wisdom , and Farore the goddess of Courage. When they created the Heavens and Earth, they left behind the Triforce, the ultimate source of power, under the protection of the Goddess Hylia. When things that are light are created, so are things that are dark. Demise, the ultimate force of evil, wanted the power of the triforce for himself to take over the world. So, he along with his minions broke through the Earth and started a long, ruthless war against the goddess Hylia herself. To protect the humans, she lifted them into the heavens where Demise could not follow, and sealed him for eternity along with the remaining species on Earth and her chosen hero.

Thousands of years pass and the humans have thrived in the Heavens. They have knights and merchants and pets called loftwings, which are really big birds that they can ride. On the day of the Wing Ceremony, where knight students take place in a loftwing race to act as the goddess Hylia’s chosen hero in the ceremony. The ceremony is where a girl, in this case Zelda, gives the winner of the loftwing race, in this case Link, a replica of the goddess Hylia’s chosen hero’s sailcloth. At this point Link learns that Zelda is the  human incarnation of the literal goddess Hylia. After the ceremony, Zelda goes missing. She supposedly left to go to the surface, which is forbidden because they think that the surface is so much more dangerous than it actually is.  Link then goes off on adventure to save her where he brings the goddess sword to its full potential and reseals Demise several times before he travels into the sacred realm, the resting place of the Triforce, to destroy Demise once and for all. Unfortunately, Demise cursed the spirit of the hero (Link), the spirit of the goddess (Zelda) and the spirit of Demise (Demise) to be constantly reincarnated and fight for all of eternity. After that Link and Zelda travel back to the future, seal the sacred realm and repopulate the surface and later establish the kingdom of Hyrule. 

Much later an evil mage by the name of Vaati is born and turns Zelda INTO STONE. Link, a childhood friend of Princess Zelda, sets off to find the evil mage to kill him and return Zelda to normal. While on his journey he finds a cap named Ezlo who looks like a talking green bird, but is actually a human turned into a hat by Vaati, and becomes Link’s companion in his adventure. Link also meets a race of tiny itty bitty people called the Piccouri who help him on his journey by giving him a sword. Link has to collect the four elements from dungeons around Hyrule to forge the Four Sword. The Four Sword is a sword that can split Link up into four versions of himself. Ultimately, Link kills Vaati I think… or he seals him in the Four Sword… I haven’t gotten the chance to play Minish Cap and no source is really clear on what happens at the end of the game. What I do know is that Zelda is saved and they return to the castle safe and sound.

Later, after these incarnations of Link and Zelda are probably dead, Vaati is resurrected and kidnaps several maidens and Princess Zelda to become his bride(s?). Link sets out with the Four Sword to fight Vaati and save all of the maidens and seals him in the Four Sword. 

Unfortunately between Four Swords and Ocarina of Time, a civil war broke out for unknown reasons. It lasted for quite a long time and had many casualties. One in particular being especially notable. Towards the end of the war, a gravely injured mother and her child sought refuge in the Kokiri Forest, the home to a race of child-like forest people who don’t age and have fairies. The mother didn’t survive but her child would grow up to be the famous Hero of Time. The Deku Tree, the guardian of Kokiri Forest and The Lost Woods, saw what would become of the child and allowed him to grow as a kokiri. When he reached the age of 10, the Great Deku Tree called for him as it had contracted a deadly virus that only Link could properly get rid of. Even though Link was successful in his extermination, it was too late for The Deku Tree. The Deku Tree in its last words sent Link off to Hyrule castle to warn the Royal family about Ganondorf, as he was the one who sought to kill the Deku Tree for the Kokiri Emerald. The Kokiri Emerald is the heirloom of the Kokiri that is protected by the Deku Tree. Link then sets out with the fairy assigned to him, Navi, to Hyrule Castle where he sneaks in through the back into the garden where he meets Princess Zelda. Together they look in the window that Zelda was looking in when Link got there. They see Ganondorf, the king of the Gerudo (a race of all women that occasionally has a man born like every 100 years who becomes their king), swearing his allegiance to the King of Hyrule. Zelda believes Link when he tells her what Ganondorf is up to and give him the Royal Family’s main secret song called Zelda's Lullaby (Linked because its so pretty) that he can play on his ocarina if he needs to get into certain areas that usually only the Royal Family could go. Then her personal guard, Impa, takes Link out of the castle and instructs him to go to Death mountain and talk to the Gorons for their spiritual stone, the Goron Ruby and then go to Zora's Domain for their spiritual stone, Zora’s Sapphire. After he obtains the three spiritual stones he has to go back to Castle Town and go into the temple of time and place the spiritual stones on the altar and open the spirit realm. On his way back however he sees Princess Zelda fleeing with Impa away from Hyrule Castle on horseback. Zelda throws Link her Ocarina, which is the Ocarina of Time (woahh game name) and Ganondorf follows not long after they disappear from view. Ganondorf vaguely threatens Link then rides away after Zelda and Impa. Link then, unfazed, goes to the Temple of Time, places the Spiritual stones in their given places, then plays the song inscribed on the pedestal. This opens the sword chamber where Link goes in and pulls the Master Sword out of its pedestal and gets sent to the spirit world. Where he unknowingly waits for 7 years until he can wield the Master Sword. During those 7 years, Ganondorf got into the spirit realm and accidentally split the Triforce, then took over Hyrule and sent the kingdom into ruin and despair. After Link gets out of the spirit realm he has to awaken the 7 sages, but technically just 6 because one was already awoke. After the 7 sages are awoken, Link then has to go to Hyrule Castle to fight Ganondorf. When Link wins, Zelda then sends Link back in time to stop any of the events from ever happening. And this is where the timeline splits into adult, child, and downfall timelines.

Child Timeline

After Link is sent back into time he has to go back and warn Princess Zelda of what Ganondorf would do. He is successful of course, but his companion, Navi left him randomly when they traveled back in time. Being lonely, he leaves to go and find her, but gets attacked by Skull Kid, a child who got lost in the Lost Woods, who steals the Ocarina of Time from Link. There’s still debate on whether Majora’s Mask actually happened or is just something that Link made up to help him cope with the loss of all of his friends and people that he knew. So I’m not going to include it except for the very beginning.

An unspecified amount of time after Ganondorf is discovered as a traitor, he is sent to be executed at Arbiter's Grounds, but it fails because at that exact moment, the triforce of power awakens in him and he kills the Sage of Water. The other sages, sent into a panic, banish him into the Twilight Realm via the Mirror of Twilight. That isn’t the end of Ganondorf however. He finds a Twili boy, Zant, who was just as power hungry as he is and puts half of his power in him for him to overthrow the current Twili(ght) Princess (Almost game name woah) and take over Hyrule, shrouding it in twilight. Link, a young farmhand in this incarnation, finds himself weirdly transformed into a wolf whenever he enters the twilight and he has to find the tears of light in each part of the kingdom to free it from twilight. At the end of the game, he beats Zant and kills Ganondorf for good in the child timeline.

The final game in the child timeline is Four Swords Adventure, and it's basically the same lore as the previous game, Four Swords. Minus Zelda being kidnaped to be Vaati’s bride. Ganondorf is reincarnated, then killed again, and Vaati is resurrected and killed. Again.

Adult Timeline

When Link is sent back in time at the end of Ocarina of Time, he leaves the people from the adult timeline to fend for themselves basically. When Ganondorf is resurrected, the people waited for the Hero of Time to show up to save them, but he never did. So, to protect Hyrule, they flooded the kingdom of Hyrule, making the Great Sea. Many many years later, Link is just a little boy on the island he grew up with his sister and his grandma on. Then his sister gets kidnapped by a giant bird so Link sets off to save her with pirates where he gets sucked into saving Hyrule by a talking boat. At the end of the game, Link kills Ganondorf, encasing him in stone at the bottom of the ocean.

Link then goes off on another adventure in a neighboring sea in Phantom Hourglass and nothing really consequential happened.

At some point a new continent is discovered and New Hyrule is established. In the next game, Link uses trains to fight an ancient king called Malladus who doesn’t show up in any other game. Link beats him and that's the end of the adult timeline.

Downfall Timeline

In the downfall timeline, Link is defeated by Ganondorf so the sages resort to imprisoning him in the Spirit Realm, which he turns into the Dark Realm after a long war called the Imprisoning War (Very creative I know). When in the Dark Realm, Ganondorf turns into Ganon, which is the pure evil version of him. In A Link to the Past, Link has to hop between Hyrule and the Dark Realm to defeat Ganon and save Hyrule.

In Oracle of Ages, Link mainly focuses on using a harp to hop between the present and the past. Whereas in Oracle of Seasons, Link has to free the four towers of the seasons to beat a resurrected Ganon.

Link’s Awakening isn’t that consequential to the Lore because it was all in the Dream of the Windfish. The Windfish is a leviathan flying fish.

Between Link's Awakening and The Legend of Zelda, the Zelda that is referred to in Adventure of link dies. Link has to defeat the demon king Ganon in order to bring peace back to the Kingdom of Hyrule and awaken the current princess Zelda. 

In Adventure of Link, Zelda is kidnapped again and Link has to save her again, but this time, there's a twist. Turns out that that previously mentioned Zelda, wasn’t dead, just asleep. So Link awakens her and now there’s two princess Zelda's out there. And Link prevents the resurrection of Ganon.