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I have quite a few fossils from underground and pardon my ignorance, but is there a way I can make them back into real pokemon like at Cinabar Island in Red and Green?
You go to the museum in Oreburgh City to revive them. It is north of the Pokemon Center. Be sure to have an extra slot in your party though because they won't be transferred to your PC if you don't have enough room.
Yeah go to Oreburgh City, go to the Pokemon Museum, and hand the very erratic man behind the counter your fossils. Walk outside, walk back inside, he'll yell at you and give you a Pokemon.