The Minish Cap is obviously the first game in the Four Sword line of Zelda games, as here we are introduced to Vaati and his backstory, namely that he was once a Minish who gained great power. The blade of the Picori is also forged into the Four Sword during the events of this game.
There is no mention of the Triforce, Ganon, sages, or other elements in this game, such as locations like Death Mountain or races such as the Zora. However, there are Gorons, and a 'light force' is mentioned. Furthermore, there is already a legend about a previous hero, though we cannot always trust the details of any past legend. These things will help us place this and subsequent games in the overall timeline.
At the end of the Minish Cap, Vaati was apparently sealed within the Four Sword and guarded over. In this game, the seal weakens over time and Vaati breaks free. Eventually, he is once again sealed within the Four Sword.
In this game, Vaati once again breaks free of his seal in the Four Sword. Link eventually defeats him as well as Ganondorf, who turns into the pig Ganon. But Ganondorf's backstory in this game is different in all other games, and it has been confirmed that it is not the same Ganondorf from Ocarina of Time. So it seems that just like Link and Zelda, Ganondorf may be reincarnated in different ages.
