Zone 0 is an initially empty zone where The Puppeteer and The Batter begin their mission. They meet The Judge here and are shown the basics of the game, including a combat and box puzzle tutorial. Once Zone 2 is purified, and the prerequisite items collected, Sugar, an optional extra boss, can be found here and defeated.
According to the Judge, "the Nothingness is a lieu of transition outside of space itself, where you can travel from one point to another at the speed of light." Essentially, it is the world map for the Batter to navigate through the different Zones. It can only be returned to by using the floating red boxes spread throughout the Zones. With the exception of Zone 0, each Zone and The Room can only be entered with a particular zodiac card. Track #2, "Silencio," of the original soundtrack can be heard here which consist of whisperings from the unknown.
Zone 1 is responsible for the production of four of the main elements as well as their processing and distribution. Upon entry from the Nothingness, The Batter is placed at the Elsen train station which can travel conveniently to the other four main areas. Damien is located to the south, Pentel to the east, Shachihata to the north, and Alma is at the center according to the in-game dialogue (although Alma is farther east than Pentel being at the end of the line for Train #1).
The Smoke Mines of Damien is where smoke is unearthed so the denizens of the Zones will be able to breathe. It rains constantly in this area. The mines themselves are filled with specters and appear to be poorly maintained, as the lights do not work in some of the deeper tunnels. Normally, regulations prohibit external visitors from entering the mines, but exceptions can be made under exceptional circumstances, "as stated in paragraph five". Zacharie is first encountered here, and Alpha is found in the access tunnel near the beginning of the level.
The Metal Farmsteads of Pentel is where cattle are raised and slaughtered to collect the metal boulders that form in their bodies. Metal of good quality is refined, formed into large spheres, and shipped to other zones, while poor quality metal is discarded and allowed to form the ground. The meat from the cattle is consumed.
The Plastic Administrations of Shachihata is where orders are put out for processed plastic to be distributed to the other zones, for use in building walls and barriers. The Plastic Administrations building is made up of 100,000 floors including the basement where a single Elsen employee has his office due to there being no more space on the higher stories. Noteworthy floors are the Ground Level, Roof, Secret Service, Lost Property Office, and Postal Service. This is the apparent origin of the spectres that plague the zone, and the first area Burnt (apparently corrupt Elsen) are encountered. Dedan also has an office here.
The Meat Fountains of Alma is where endless streams of meat of unknown origin fill enormous metal pools. The Elsen here must bottle the meat before it overflows. The fountains are navigated by means of Pedalo duckboats, and full of serpentine Troquantary. Dedan's main office is at the center of the fountains, and it is here that he is fought.
Zone 2 is a residential zone, overseen by Japhet. It is known by the alternate names "Bismark" and "The Pink Fortress" due to its bold magenta color. A circular path surrounds it and branches off into the amusement park, residential area, and shopping mall.
At the center of Zone 2 is the library, a very large building containing real books, fake books, and specters. The Elsen inhabiting the zone have grown discontent and paranoid, and many of the shelves are full of fake books that cannot be torn or damaged, but in the upper floors the Batter can find books that are still readable, and a puzzle involving replacing several missing pages. One page is held by an Elsen standing near the entrance to the park, who will give it to the Batter in exchange for 100 credits. Japhet is initially met and fought in floor 4 of this building once the puzzle is completed, and is fought again later on the roof. Omega is found after the initial battle with Japhet on floor 4.
The shopping mall is located north of the library. It is a desolate place that appears to have been largely abandoned, full of empty stores and specters, a well as the infamous whale enemy. The walls are papered with advertisements. Zacharie is encountered here again, as is the Judge, and Valerie/Japhet can be seen patrolling in a corridor. The interior of the mall is a maze that loops unless the Batter takes the correct paths. Upon reaching the end, a pedalo summoning point will be found, and the park can be accessed.
The amusement park is located to the west of the library. It appears to have been closed off, and several Elsen standing near the entrance remark upon this fact, but guests can still be found inside. It is reached via pedalo that is summoned from the shopping mall. The park contains a roller coaster, a balloon popping game, and a pedalo boat ride. The Elsen within the park, however, are all too nervous and frightened to enjoy the attractions.
Navigating the pedalo ride and reaching the switch is necessary to open up the coaster. The Batter can ride the coaster and obtain a photograph with the statue of Zacharie, the park's owner, in order to gain access to Zacharie's office and the items within. Upon winning the balloon popping game, the defeated Elsen will become a Burnt and attack the Batter, prompting the park's guests to panic. Upon defeating the Burnt, the Batter will win the necktie necessary to open the residential area.
The residential area to the east contains homes, several of which are locked and can only be opened with combinations. Japhet appears here and orders his specters to attack the residents, and the Batter must clear the area of enemies within 4 minutes (disregarding battle time). The Elsen kick him out once he is done, because his bat is too dangerous a weapon to be allowed inside. There are three bunkers here, each of which require a code to be accessed: 1402 for the southwest bunker, 1805 for the northwest bunker, and 1709 for the southeast bunker (which can only be accessed after the zone is purified). After the Batter is expelled from the residential area, the Judge arrives and asks for help for Valerie (he joins the Batter at this point, but does not fight alongside him).
Finally, the Batter can access the remaining floors of the library and fight Japhet on the roof of the library.
Zone 3, also called Vesper, is characterized by its many refineries and industrial atmosphere, and ruled by its director, Enoch. It is here that sugar is produced, a sweet and addictive compound fed to the unwary Elsen that work there. Zone 3 may be where the dead of the other zones are sent for disposal, but this is not confirmed. The Elsen inhabiting zone 3 seem out of touch with reality, dreamily speaking of loving their jobs, and of their obsession with sugar. So great is their addiction that they will destroy spectres to protect it, and become some of the strongest Burnt in the game.
Similar to zone 1, zone 3 is connected by way of a train system. Area 1 contains the cafeteria and dormitories. The cafeteria is swarming with spectres and can only be navigated with the help of a stamped note the Batter finds upon entering. Epsilon is found here, as well as Zacharie, who is present throughout the level.
Area 2 contains the treatment rooms, and many switch puzzles. It also contains a large amount of sugar in piles in the warehouse.
Area 3 contains the entrance to the sewers, and the furnace where bodies are burned. In order to access it, The Batter must jump down the smokestack and start the "Game of the Mortal Fall." It appears to be raining ash in this area, most likely from the furnace.
Area 4 is a series of hallways patrolled by Elsen in lab coats, and contains Enoch's office, as well as the strongest Burnt in the game, the Pastel Burnt. Many of the doors are locked, but Batter may access a choice few. One appears to have been bricked up for no apparent reason which disappears after the Zone is purified. The Batter faces Enoch here, first in his office, and then in the train tunnel.
After a zone has been purified, the Batter may return to the zones to discover a world devoid of almost all life and color and will occassionally cross paths with the Secretaries, whose existence was never really explained. Track #5 "Not Safe" in the original soundtrack can be heard as the player traverses through the purified zones. The layout of the zones have also been slightly modified cutting off some areas and providing more puzzles. At the end of the longest path of each purified zone, there is a room with a giant ten of spades painted on the back wall. The room always contains a red cube and two chests. Inside one of these chests is a bizzare object. In Zone 2, The Judge can be found at the top of the library mourning for the lost of Valerie, and a lone Elsen appears inside a bunker of the residential area.
"The Room" consists of a bedroom and a hallway and changes with each chapter starting from 5 and going backwards. In a recent painting by Mortis Ghost, The Room is shown to be located underground. (More information on its own page. Caution - incredibly spoiler-heavy!)
In Chapter 5, you encounter an army of teddies.
In Chapter 4, you meet the Tall Mister, The Bird, and The Big Mister.
In Chapter 3, you have three different saves to choose from.
In Chapter 2, you read a comic.
In Chapter 1, Zacharie greets you before you face the final boss.