Atlantis is an area accessible from the Grand piano in the Snowy Pipe Organ.
Atlantis is a large area at the bottom of the ocean. Coming from the Snowy Pipe Organ, the piano connects to an opening in a tall field of coral, with bubbles rising up from the sand. Shoals of fish will pass by periodically.
There are two paths leading up and down from the piano.
Going down from the piano will take you to the Reef, and taking the path upwards will take you to a throne room with three strange creatures and a big pink chair at the top of the room. If you use the Fairy or Child effect at the hole in the wall behind the pink throne you can crawl through it and access the City.
Using the Fairy or Child effect at the hole in the wall behind the pink throne will take you to the city. There is a road and a number of tall buildings here. You can also see Tako Otoko standing in the open. By going through one of the doorways, you'll come to the entrance to Tapir-San's Place.
If you continue right, you'll reach a long road populated by blue figures (some of which are just floating in the foreground). Weave in and out of them to keep going right and you should reach the Underwater Amusement Park.
Going down from the grand piano will take you to the reef. Coming out of the coral field, there are a number of fish swimming around this area. The less dense part of the coral field to the sides of the entrance hides a hidden path, which will take you to The Trench.
Not far from the entrance, there is a strange melted-looking head in the sand. If you equip the Eyeball Bomb effect near it, it will smile at you.
There is also a large group of small rocks arranged in the shape of Urotsuki's head towards the middle of the area, with what appears to be a ghostly image of Urotsuki sitting in the middle of them. If you have the Glasses effect equipped, a child version of Urotsuki can be seen standing in front of it. Through gaps on the west side of the rocks, it's possible to get closer to them. When you interact with the child-Urotsuki from the side with the Glasses effect equipped, a short scene plays where she looks at you, and proceeds to walk over to the ghostly image before vanishing.
At the far south of the reef, there are many dwellings made of sand, an exit to the Realistic Beach, and a large sea sponge that reacts to the Penguin and Wolf effects, allowing the player to unlock Wallpaper #195. This sea sponge can be killed with the chainsaw and does not seem to revive after waking up.
At the very bottom of the reef there is a set of steps by a monochrome sea sponge leading down to an area separated by a small trench, with a large shadow on the other side. You can cross over the trench using the Fairy or Penguin effects, and walking down into the shadows will take you to the underwater section of the Flooded Baths.
The Trench Overlook
The trench overlook is a small sub-section of the reef that can be accessed by navigating through the coral northeast of the entrance from the piano. Aside from the trench itself, this area contains only a bench for Urotsuki to sit on at the far east end, as well as an exit back to an isolated section of the reef just southwest of the bench. This isolated area contains a red sea sponge that will tint the entire reef red when interacted with; while the reef is red, a uniquely shaped tree of coral will appear across from the trench that teleports the player to the Scorched Wasteland, with no direct way to return.
Each time Urotsuki sits down on the bench, there is a chance that a small bus will pull up midway over the trench. If Urotsuki walks up to the door, it will slide open and let her on board. Inside the bus all the seats are empty, save for a dark bus driver's silhouette wearing a black cap.
After spending a certain amount of time on the bus it will start moving, going over an occasional bump on the way. Once the bus has stopped, Urotsuki can get off through the front door into the Botanical Garden.
At first there appears to be nothing on the west side of the trench, but if you equip the Penguin effect you will see some bubbles floating out of the trench. Interacting with them will let you swim down into the trench and move along the seabed, until you reach the entrance to an underwater cavern at the end.
Inside, the cavern leads deep down into the ocean, until you eventually emerge into the bio-luminescent Star Ocean (深海1, Shinkai 1, Deep Sea 1). (The only 2 effects that seem to work inside the trench and star ocean are the Penguin and Spacesuit effects)
If you equip the Fairy or Penguin effects you can cross over to the other side of the trench, which is just as empty as the lower side, only containing a long impassable path covered in rocks and a bench and large vending machine near a crack in the ground that can be found by navigating a small maze of coral and pebbles on the east end.