go to the end of cerulen cape then talk to Misty. go back to cerulan city and she will be at the gym.
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Because Misty is not at her gym, you have to find her up at Route 25.
Nobody knows actually.
top left tube
she is never in the gym she is usually in the kitchen tho.
It's just like the old silver version you go up on the bridge and find a guy that is standing next to misty and after you either talk to him or walk a certain distance near him,misty will walk away and she will reappear at the gym.