His body doesn't have anyone in it, it's just an empty shell looking for it's soul.

Link watched, somewhat unsettled, as his body walked toward him, a blank, empty look on it's face. Then it stopped directly in front of him. Staring at him. Growing annoyed, Link asked harshly, "Ruto, is that you in there? Are you playing a joke on me or something?" No response. "Do you think you're me or something? Because I am the only Link, the Hero of Time!" Nothing. Link stamped his foot on the ground, angry. "What is wrong with you?!" He might as well have been talking to a wall. That was when Link caught on. "Wait, you're nothing, aren't you?" he said with a comprehending smile. "You're just my empty souled body, and you wanted to find me again, right? Good, that makes this much simpler." Link reached into his body's pocket, blushing and trying not to grope his original form more than was necessary, until he found the Ocarina of Time. "Perfect!" With that, Link started to play the Prelude of Light, so they could teleport back to the Temple of Time. It was much harder playing it with Ruto's smaller hands and webbing fingers, but he managed it. And yet, nothing happened. "Argh!" Link threw the instrument on the ground in anger, throwing a temper tantrum. "The ocarina only works with my body! That isn't fair! I want to use it! Me!" Taking a breath and calming down a little, Link picked up the ocarina again and gave it to his body, hoping this would work. "Listen, um, body, play the Prelude to Light." To his surprise, it worked, giving new meaning to the term 'muscle memory'. As it started to play, Link made sure to grab on tight to his old self and teleport with him to the Temple of Time, and once there he immediately stalked over to the fairy fountain where he had made that stupid wish to begin with.

Inside the fairy fountain there were fairies everywhere, but no sign of the great fairy. Upset, he commanded his body to stand over the symbol on the floor and play Zelda's Lullaby, which it did. Nothing happened. That was the last straw. The next few minutes were a blur as Link ranted, raved, screamed, demanded, and in general pleaded to return to his old body. Once that was done, Link knew that none of that would work. Together, he and his body went to Hyrule Field, called Epona, and he had his body ride them both to Kakariko Village.