Here's a trick to temporarily get Navi stuck in the Temple of Time. However, I can't find anything special you can do after you've done this trick - it must just be a glitch in the game. If you can find something useful about this cheat, please tell me about it. Anyway, here's how to do it.

Go to the Temple of Time as an adult and approach the stone holding the three spiritual stones. Read the inscription on it, and then do a backflip on it from the side where Link's back is to the pedestal of time., so you are in between the Goron's Ruby and the Zora's Sapphire, facing the Kokiri's Emerald. Now play Saria's Song and hop off. If you did it right, Navi should be stuck there. Walk around the Temple of Time, and you'll find that it's a lot darker. As soon as you leave the Temple of Time, Navi will be back with you.

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