The Legend of Zelda is a very confusing, unorganized series that requires a lot of thinking to quite understand how all these games fit together into one story line. Some may say there is no direct story line and that they are loosely linked; but there are some still out there, still researching and theorizing timelines among the games, those who still believe that there is a Zelda timeline. I am one of those people, and I strive to find the true Zelda timeline. So let's begin.
The first mention or questioning of the Zelda timeline was after Ocarina of Time was released. This game brought new opportunities to think about how the games are connected. Miyamoto released the actual timeline after that game was released. He simply put everything the order it came out, but put Ocarina of Time in the beginning. I am not sure if all the games in the past still matter in the timeline because of their age. It could be possible that they are forgotten and are no longer any part of the timeline. So to start out with my timeline theory, I begin with the more important games that are in the timeline for sure, then I put in the least important where they would go if they existed. After a long bit of research, I have concluded something that could be as close as I can get. There are other things I do not know that no one knows that makes this difficult. I do not know if the timeline is split or not, but right now I believe it is split because Miyamoto has talked about the split timeline himself. I also do not know if the four swords series is relevant to anything else going on. I am also not sure where it would go in the timeline, because they released it was before Ocarina of Time, but this seems to make little sense; But with enough thinking I could make it make sense. I do have other thoughts in mind but I can't share everything. There are many topics and debates over this timeline that I can't explain now. I merely wanted to point out what was important to me so I could show an understanding of my timeline. It may not be correct, it may not be even close to whatever it is this game was created to be, but this is what I have concluded and this is what I believe.
Minish Cap- This, to many people, is the first game in the series. It is perfectly possible, since there is no Ganon. It explains a hero of men, not a hero of time, and has Vaati, who does not show up in any other games, which could mean he is dead during the future games. I have also heard of the theory that this is where the hat comes from, but it is very weak evidence. The more I think about it though, it does seem like this is the only game that includes any origin his clothes. At first I thought his clothes game from the Kokiri tradition, but I do seem to forget that when the games were not made in order, they were not thought out perfectly. So in this game is the very first, true Link. He uses the Picori sword to defeat Vaati, and it eventually becomes the legendary four sword. He seals it away for future use, and that's the end of that.
Four Swords/Four Swords Adventures- I think these two are the same thing. Four Swords isn't a real game, I know that. It was multiplayer only which meant not everyone could play it. It was just a bonus with Link to the Past for Game-boy Advance. Four Swords Adventures, though, was a real game. It comes only a few years after Minish Cap and starts with the four sword sealed away. Link finds this sword, and uses it to kill Vaati for good. But then something confusing happens. Ganon shows up. This is now the first appearance of Ganon, with no Triforce. He is just a pig with power. It could be said that Ganon was a minion of Vaati and that Ganon became the main villain after Vaati was defeated. It is not clear what happened to the four sword, but I do know that the master sword is how Link defeats Ganon. So Ganon is defeated, and decides to go seek out the Triforce at the sacred realm where the master sword is sealed away. The second link in this game is dead by the time Ganon finds it, and by then the third Link is born. The third Link is the first Link to be chosen by the Triforce.