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He isn't IN Sci-Lab Square, but the Sci-Lab Area OUTSIDE the Square. He starts out in Sci-Lab 1, but after Megaman and Lan botch the acting, he resets in Sci-Lab 2, where you actually get to battle him. These aren't large areas, so if you look like you're really looking, you'll find him. Now go beat that bad, bad navi. Sounds a bit wrong, doesn't it?

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Q: Where is the bad navi in scilab square on Megaman 3 blue?
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