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Captain Stern is on the top floor of the museum in Slateport City.
In the Slateport museum.
While in Lilycove City, you can find Captain Stern in that museum place where Team Magma/Aqua are standing by. I forgot how to get rid of them, but once you do, you can find Captain Stern in that museum place I mentioned.
Capt. Stern is not in Pokemon Leaf Green. He is only in Pokemon Ruby, Saphire or Emerald.
You can find captain stern if you finished your mission on magma hide out then you can go to slatefort city to find captain stern your mission now is to defeat team aqua in seafloor cavern in route 128 after you defeat the gym leader in mosdeep and team magma in the mosdeep sapce center then you go to steven to get the hm dive