Jolly Roger Bay

Jolly Roger Bay is the first underwater course. It is known for its highly praised song and difficult 100 coin star. It features quite a few unique assets such as the ship, the stone pillars, and the unagi eel.

Geography
As mentioned previously, Jolly Roger Bay is a mainly underwater course, with not much above water. The starting area is a beach with a few rocks, and immediately visible is a cannon, some stone spires, and, in the second mission onward, an abandoned pirate ship. Underwater has fish, clams, even more rocks, and the entrance to a cave. The cave has strange collapsing stone pillars and electrocuting treasure chests.

Missions

 * 1) PLUNDER IN THE SUNKEN SHIP
 * 2) CAN THE EEL COME OUT TO PLAY?
 * 3) TREASURE IN THE OCEAN CAVE
 * 4) 8 RED COINS ON THE SHIP AFLOAT
 * 5) BLAST TO THE STONE PILLAR
 * 6) THROUGH THE JET STREAM
 * 7) 100 COIN STAR

Unagi Caves

 * Main article: Unagi Caves

Unagi Caves is a supposed secret area in Jolly Roger Bay. How to enter varies from different reports, but they always mention going through the tunnel in which the unagi lives.

Who Was Here Before?
In Jolly Roger Bay, there is evidence of people (probably pirates) being there before Mario, yet it is never acknowledged. For instance: The treasure chests, pirate ship, and collapsing stone pillars. It is clear that people were there before, and even left a sign. How did they get there? The water is surrounded by rock on all sides, so it doesn't seem likely that a boat could just sail over there. One theory is that, because there is an invisible and intangible ship in the sky, the boat was supposed to be seen falling from the sky for some reason. It is likely that there was no one there before, though, because the paintings worlds are allegedly created by bowser.

Blurps
Blurps are enemies in the Super Mario Bros. series, first appearing in Super Mario World, that can supposedly appear in Jolly Roger Bay. They are green and white fish with goggles that appear similar to those worn by Bubs. In manifestations where they appear, they can be reskins of Bubs, or have a unique ability, such as charging towards the player or shooting a bubble that an damage the player.

Mist
When selecting the star Plunder in the Sunken Ship, a thin layer of mist will be covering the water inside the level. The skybox is also darkened, giving the appearance of stormy weather. Once the player completes the level and collects the star, this mist and dark sky will mysteriously disappear. Upon entering the level again, the sky will be clear as usual, and the mist will be gone. There is no way to make it reappear on that save file, even if they replay Plunder in the Sunken Ship. The purpose and meaning of this mist is unknown, but it could be theorized to have something to do with the ship being raised after collecting the star.

This phenomenon does not appear on the Nintendo DS remake.

The Ghost Ship
Not to be confused with the Haunted Ship level in the Peaceful Grounds.

The Ghost Ship is an unused object found floating in the sky of Jolly Roger Bay. It is an invisible, collisionless clone of the pirate ship in the Plunder in the Sunken Ship mission. When it is edited to be viewable in the game, it disappears as the player walks towards it, similarly to Toads which disappear as players walk away from them. In some personalized copies, it can reportedly appear in the sky. Some have claimed it falls from the sky and becomes the ship in Plunder in the Sunken Ship, or appears if they somehow manage to shoot down the airship in Rainbow Ride, implying that Rainbow Ride takes place above Jolly Roger Bay. Some have also claimed that the Ghost Ship is an accessible sub-area of Jolly Roger Bay or an entire new level. The Ghost Ship can reportedly be a clone of the pirate ship sub-area, or be a unique area with the Ghost Ship standing up and fully explorable. Notably, a type of Boo referred to as a Buccaneer Boo, a Boo dressed as a pirate, can reportedly be found on the Ghost Ship that can either act identical to Boos or have a special ability such as using a sword to attack the player.