Gold versiom
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The ship (S.S. Aqua) can only be used on certain days of the week and for certain functions only.
To use the SS Aqua you'll need the SS Ticket from Professor Elm (go to the Hall of Fame). Then you can only use the ship to go from Olivine City to Vermilion City on Mondays and Fridays only.
You can also make a trip to Kanto. The first time this can happen on any day, but for subsequent trips the SS Aqua sails from Kanto to Johto every Sunday and Wednesday, and sails from Johto to Kanto each Monday and Friday.
You can also find and battle trainers while on the ship!
For more questions for Pokemon Gold check out the question page where you can search or ask your own question.