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If you mean that by leaving link when battling ganondorf (1st part) then it is because ganondorf uses part of his triforce power to make it so Navi can't lock on to him. all you have to do for that part is him the energy orb with your sword. In other words ganondorf uses his power to keep navi out of the battle. If you mean why does navi leave after the game ends, ts because navi was only meant to join link and help him save hyrule, she cant stay with him because hes a hylian not a kokiri, but im sure they talk sometimes.

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16y ago

What else can I help you with?