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At the Weather Institute, you are given a Castform after getting Team Aqua/Magma to leave. Did you use the gift Castform at all, or did you immediately box it?
I think in ORAS, you can fly with him in your party on the Latios/Latias to go get Palkia/Diagla in a dark cloud if I remember correctly? IDK google the method. So yah, box til you get the Eon flute....then box again. Still, what a nice gesture of the Weather Institute. I honestly thought it was nice of them. I think I boxed in the original 3rd gen too, but I forgot. So long ago.