Leave her at the Altar!
This is another glitch I call the Navi's stuck glitch, which you get on the altar with the Spiritual Stones on it. You have to be an adult. Get on the altar, read the inscription, get between the Goron's Ruby and Zora's Sapphire, looking at the Kokiri's Emerald, and Play Saria's Song. Press Talk to Saria, It'll only say the first line, and then Navi will be stuck. Play the Song of the Sun, and You'll be at the place you came in from. Run around, Navi doesn't come out when you run anymore, unless you get by the place near the spiritual stones with the green arrow.
