In the games
This ship contains many Pokémon trainers looking for a Pokémon battle, including many Gentlemen and Sailors. Battling through the ship is easy, however, because a room is provided with a bed that acts like a Pokémon Center, restoring all Pokémon onhand to full health. Before reaching the captain's cabin, players will encounter Blue, and must battle him.
Once Blue is defeated again, the player will be able to enter the Captain's quarters, where they will find him seasick. By choosing to help him by giving him a backrub, players will be able to get HM01, Cut.
Once the captain is healed, the S.S. Anne will sail away the moment players exit the ship, never to be seen again.
RumorsIn Pokémon Red, Blue and Yellow, as well as their remakes Pokémon FireRed and LeafGreen, there is a truck which appears in the S.S. Anne's port which serves no evident purpose except as scenery. With scenery being very sparse in the Generation I games, and this being one of the few sprites with no other purpose than to exist in one spot, fans began speculating that another purpose existed for this truck, and that it could perhaps be moved with Strength. Thus, a popular rumor sprang up that a Poké Ball containing Mew could be found underneath. HM for Strength could only be obtained after getting Cut, which required the S.S. Anne leaving. Players found ways around this by trading Pokémon knowing Cut to other games which did not have the HM. The rumor was proven false.
Another method to prevent the ship setting sail was to challenge a Trainer after obtaining Cut, and losing the battle on purpose. The player would be teleported to the Pokémon Center in Vermilion City, and the ship would not leave the dock, making it accessible later in the game when the player had obtained Strength/Surf.
In the Generation III remakes of Red and Blue, the truck is still present, however, there is actually somewhat of a point to get to it this time around. On the pier it is on, if the player walks down a bit, they can find a hidden Lava Cookie, unavailable until later in the game. This could possibly have been put into the game as a reference to the old rumors.
After the S.S. Anne leaves Vermilion City, it never returns. However, some players spread another rumor; by defeating the Elite Four 365 times, supposedly you were able to make the ship return and possibly battle new Trainers on board. This was supported by an NPC in Pokémon Red and Blue explaining that the ship was a luxury liner for Trainers that visited Vermilion once a year. However, there was no way to make time pass in the Red and Blue versions, so this was obviously just a hoax to get people to try something tedious and stupid.
In the anime
Ash, Misty and Brock boarded the ship after two schoolgirls, who were actually Jessie and James in disguise, offered them free tickets. This was part of a Team Rocket plot to steal the Pokémon of all trainers onboard. However, Ash and his friends enjoyed the St. Anne, which provided large amounts of food for people onboard and allowed Pokémon battles below deck. While onboard, James was swindled by the Magikarp Salesman into buying a Magikarp in a gold-plated Poké Ball, and Ash traded his Butterfree to a Gentleman for a Raticate.
Out on the open ocean, Team Rocket, including Jessie, James, Meowth, and a number of Team Rocket Grunts began taking the Pokémon of everyone else onboard the St. Anne by force. Ash led a counterattack against the Rockets, leading to a large battle and many of the members of Team Rocket being 'blasted off' through the side of the ship.
Afterwards, the St. Anne started taking on water, and the passengers had to be evacuated. Ash delayed evacuating to trade back the Raticate for his Butterfree, and while rushing to escape the St. Anne jerked and knocked out Ash, his friends, and the Rocket trio. When they awoke, the St. Anne was upside down and underwater, balancing on a seamount.
The two groups fought at first, but Misty took charge and began directing all of them in an emergency escape plan before the ship fell into the depths of the sea floor. Since the ship was upside down, they would need to escape through the thinnest point in its hull, which Misty knew was in the engine room, having built a model of the ship herself. They made their way through the ship to this point, and then Ash ordered his Charmander to burn a hole in the hull. With the help of Squirtle, Goldeen and Starmie, Ash and his friends were able to swim to safety, while Team Rocket nearly drowned since all they had to rely on was James's Magikarp, which could only Splash around on the floor.
Once everyone was offboard, the St. Anne's balance tilted, and it fell off the seamount, down towards the abyss, never to be seen again.
In the manga
In the Pokémon Special manga
The S.S. Anne is a huge cargo ship owned by Lt. Surge that arrives in Vermilion City port once every month. It has appeared in Danger: High Voltorb and Buzz Off, Electabuzz! supposedly transporting materials from Vermilion to Cinnabar Island; the truth is that it is used to transport the citizens's Pokémon, kidnapped by Surge and his sailors. Voltorb, Electrode, Magnemite, Magneton and Electabuzz are some of the Pokémon spotted aboard.