Link was sent back in time seven years so that he could live a life he would have lost otherwise being forced to stay within the Sacred Realm. When Link returned to his Childhood, he lost Navi and began a quest to locate her. Along the way, Link was accosted by the Skull Kid under the influence of Majora's Mask and was lead into Termina, an alternate dimension to Hyrule. When he saved that world, he resumed his search for Navi.
This Link is later seen again in "Twilight Princess" as the Hero's Shade, the spirit that teaches Link hidden skills because the Hero of Time died with the regret of not passing on his skills to a new generation.
Link never found Navi, and possibly died in the search.