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DanneSandin said:
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What?! The stories continued after that game??? What happened to him???

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I don't know.

He is personally mentioned in the prologue of the Wind Waker, several times during Twilight Princess and because of what is now said about it in Hyrule Historia, you could say it's implied in the prologue to ALttP that he died at some point before that (though ofcourse that was never written as such back then). Plus the ending to Majora's Mask doesn't exacly wrap things up.

So now there are explanations for the Wind Waker and A Link to the Past stories, but all the references to him in Twilight Princess don't. Some people believe the 'Hero's Shade', the ghost-character that teaches you new moves inside a dream world, is in fact the Hero of Time, mainly because he knows so much about that Link while most of his adventures didn't actually happen for the TP timeline due to timeline issues caused in OoT. Personally I don't think it is Link, but if it is, how? What happened there? It gets quite complicated because of the split timelines and stuff to figure out what happened prior to what game and what in TP could reference the OoT/MM Link though. Like the green tunic in TP, said to have belonged to a 'Legendary Hero', or the Hero's Bow, said by the Gorons to have belonged to one that helped them centuries ago.

Concerning Majora's Mask, the game starts with Link searching for 'a friend', of whom it can be assumed is Navi the fairy since she's abscent, while riding through a dark forest. At the end of the game however, Link is seen riding off through the same woods someplace else, presumably continueing his initial quest before he got interupted by the Skull Kid. This leaves a very open end.