after you beat the elite for the ferry is complete and captain stern is the captain of the ferry (i think check to find out)
you go into the aquarium place, and he will be there.
Head to slateport city and go to the SS tidal captain stern will be nearby.
You deliver Devon's Goods to Captain Stern who is in Slateport City's museum.
Captain Stern is on the top floor of the museum in Slateport City.
Go back to Slateport town. Inside the ferry building, you will find captain stern and the submarine being robbed by Team Aqua.
first, go to the shipyard. Captain stern isn't here though. Talk to the man that you first come across that seems to be staring at a piece of paper. He'll say that he is called Dock and then tell you that Captain stern is at the museum. Finally, you know where he is! Go to the museum at the east of town, then talk to the man on the second floor. He is Captain Stern. He'll take the goods,thank you,and arrange to leave.Before he can move,2 members of team aqua will come in and try to steal the goods.Battle them,and when you defeat them both,the aqua leader will come will come,give you a brief warning and leave. .
he will be at slatport city after you find the team magmas hideout having a interview
Go to the shipyard, and talk to the guy standing by the table with a map on it. He will tell you Captain Stern isn't there. Leave the shipyard, and go into the museum. Go to the backroom, and talk to the scientist. He is Captain Stern. Team Aqua will come inside, and be prepared for two battles. After you beat them, you can give the parts to Capt. Stern. Hope this helps! :)
At Staleport City
The captain went to the stern of the ship to see if anyone was following them.
he's not in there! he's in slasport city his worker is in the abandoned ship and he asks you to find the generator or something i forgot then you have to find it and then you go talk to him and he will tell you to go to captain stern and then go to slaport city and then he will trade you for something. hope i helped :)