From Bulbapedia, the community-driven Pokémon encyclopedia.
Vermilion Harbor is a harbor which can be found in Vermilion City, Kanto. It has appeared in all generations of the Pokémon games (except for Gen V), the anime and the Pokémon Adventures manga.
In the games
The S.S. Anne sitting at the dock of the harbor
Generation I and III
Vermilion Harbor has only one purpose in the first generation games, Pokémon Red and Blue. The luxury cruise vessel, the S.S. Anne, is docked there, and aboard is a man who will give HM01 (Cut), which is necessary to progress further in the game. After the player has departed the ship with the HM, it will continue on its voyage around the world.
While the S.S. Anne remains an aspect of gameplay in Pokémon FireRed and LeafGreen, the harbor also has a new vessel docked. One of the Seagallop Ferries will wait at the end of the dock once the Elite Four has been defeated and provide transport to the Sevii Islands.
In the original Pokémon Red and Blue, the player will need the S.S. Ticket from Bill to tour through S.S. Anne. In Pokémon Gold and Silver the harbor was modified, but still has its own purpose; the player will need to defeat the Elite Four to tour S.S. Aqua.
Generation II and IV
Three years have passed since the events of Red, Blue, Yellow, FireRed, and LeafGreen, and over that time the harbor's appearance has changed. The S.S. Aqua travels here from Olivine City in the Johto region, and is one of two quick ways to travel between the two regions. It will only come on certain days though; those days being Wednesday and Sunday; or for the remainder of the week the harbor is empty.
In the anime
The Vermilion Harbor has appeared in many of the episodes located in Vermilion City. The first time it was shown, in Battle Aboard the St. Anne, Ash, Misty, and Brock boarded the S.S. Anne, which sank due to an intervention by Team Rocket. The wreck of the ship is believed to remain at the bottom of the harbor.
In the manga
In Pokémon Adventures, the Vermilion Harbor is the setting of six rounds beginning with Ekans the Ecstasy through to Breath of Dragonair Part 3. In these chapters, the S.S. Anne sinks to the bottom of the harbor. Yellow is also told the legend of the harbor by the Pokémon Fan Club Chairman: apparently, four stones lie at the bottom of the harbor and never lose their powers of starting a Pokémon's evolution. This story is present only in Pokémon Adventures; Surfing in the harbor does nothing for the evolution of Pokémon in any game, and no sunken stones have been mentioned in the anime.