The Bottle Ship is a spacecraft designed by the Galactic Federation in order to cultivate bioweapons against Federation protocol in a series of simulated environments known as sectors, each based around a dome and divided into four blocks. This project as well as a secret project to mass-produce Metroids is headed by Madeline Bergman. Samus Aran and the Galactic Federation 07th Platoon, the latter commanded by Adam Malkovich, arrive here after receiving a distress signal known as "Baby's Cry," so named because its issue implies a sense of urgency and a need for attention.
- Main article: Main Sector
The Main Sector is the largest sector in the facility and is the only sector not to have a simulated environment; it is entirely mechanized. A portion of it includes the Landing Site for Samus's Gunship and the platoon's transport ship, which is located slightly in front of Samus's ship. Other notable rooms include the Control Room, where the Bottle Ship's operational equipment is housed and from whence the platoon receives its orders (and from whence Samus receives hers), the System Management Room, which includes a terminal that provides power to the sector (initially off-line), the Control Bridge, which houses the facility's navigational equipment, and the Residential Quarters, which is empty when explored but presumably housed Bergman and her staff. It also includes a large elevator known as the Main Elevator, which provides access to all sectors except for Sector Zero.
Sector 1 (Biosphere)
- Main article: Sector 1 (Biosphere)
The Biosphere is the first simulated-environment sector encountered on the Bottle Ship. It is a jungle environment, featuring a wide variety of flora and fauna that have adapted to its warm and humid climate. Vines pervade its many corridors, and it is subject to incessant but pleasant bouts of rainfall. It also sports a small river, a lake, and a waterfall. Scattered throughout the sector are terminals that can toggle its environment on and off. Its most notable location is the Exam Center, housed in the Biosphere's test area, where Samus Aran, the platoon, and Adam first become aware of the plot to create bioweapons. The body of Lyle Smithsonian is found a few feet from it.
Sector 2 (Cryosphere)
- Main article: Sector 2 (Cryosphere)
Despite its number, the Cryosphere is the last simulated-environment sector encountered. It is designed to house creatures adapted to frigid temperatures. The sector features a continuous snowfall, and its terrain consists of large stalactites and other ice structures as well as icy platforms. The latter are often found floating in one of the sector's many lakes, a few of which are frozen solid. It also contains the only known entrance to Sector Zero, and the rooms leading to it feature bizarre gravity fields. The sector even contains a victim of Metroid predation, a Gigafraug, seemingly impossible considering that Metroids cannot survive cold temperatures and were completely annihilated after Samus's last mission. MB is first sighted here, and Samus becomes aware of the presence of an assassin within the platoon.
Sector 3 (Pyrosphere)
- Main article: Sector 3 (Pyrosphere)
The Pyrosphere is the second simulated-environment sector encountered and houses creatures adapted to extremely high temperatures. It features an active volcano and mainly consists of a sea of lava with rock platforms scattered throughout, rendering it deadly without proper protection. Its only other notable features are a hollow, spiraling mountain with a pool of lava at its summit and the Geothermal Power Plant. Anthony Higgs seemingly meets his demise in the latter at the hands of Ridley shortly after being rescued by Samus from the Rhedogian, which first appears in the Cryosphere. K.G. Misawa's frozen corpse is also incinerated in this sector by the assassin within the platoon, and Samus's contact with Adam is severed.
- Main article: Sector Zero
Its existence known only to Madeline Bergman and her staff, Sector Zero is apparently modeled after Tourian. It contains unfreezable Metroids and the prototype for an artificial intelligence based on that of Mother Brain, an intelligence that was later refined to create MB. Adam Malkovich dies here, venturing into and damaging the sector, causing it to detach from the Bottle Ship and explode. It is the only sector Samus does not explore, as she is shot in the back by Adam's Freeze Gun and knocked unconscious before she can, leaving her in her Zero Suit.
Bioweapon Research Center
- Main article: Bioweapon Research Center
A complex accessed from an elevator in the Biosphere, the Bioweapon Research Center is where Samus learns the details of the Federation plot to create bioweapons as well as the plot to propagate Metroids. Ridley is killed here by a Queen Metroid. The body of James Pierce is discovered here, presumably killed by MB or a Desbrachian, and MB herself dies here. Madeline Bergman is found in one of the holding cells in Room MW, which also contains six specimen tanks and houses the Queen Metroid. Room MW is also preceded by several corridors populated by sentry drones and Rinkas.
- Many similarities exist between the Bottle Ship and the Biologic Space Labs research station. Both stations consist of specialized sectors Samus must venture through, both involve searches for survivors, both also sport discreet Metroid testing supported by the Federation, and both hold the entirety of their respective games.
- "The terraforming capsule colony designated as BOTTLE SHIP is currently under the administration of the Galactic Federation. The ship supports animal specimens from various ... the purpose of biological-weapon research. There were originally two other BOTTLE SHIP, designed for use by interplanetary colonists by the Space Development Corporation. After long years of use, the first two ships were retired, and the remaining ship was given to the Galactic Federation. After extensive refitting, the ship was made able to sustain three distinct closed habitats, each designed to preserve various specimens collected from different planets for research and development in military-technology applications." —Exam Center computer (Metroid: Other M)
- "The structure of each sector is centered primarily on a cavernous dome. In order to maintain the structural integrity of the whole within the limits of material strength, each dome structure is divided into 4 blocks, for a total of 12." —Exam Center computer (Metroid: Other M)
- "Code name: "Baby's Cry." A common SOS with the urgency of a baby crying...The nickname comes from the fact that the purpose of the signal is to draw attention." —Samus Aran (Metroid: Other M)
- "Sector 1 Biosphere
This section has been reserved for the care and feeding of animals that can survive in an artificial atmosphere of warmth and humidity." —Exam Center computer (Metroid: Other M)
- "Sector 2 Cryosphere
This section has been reserved for the care and feeding of animals that can survive in an artificial atmosphere of extreme cold." —Exam Center computer (Metroid: Other M)
- "Sector 3 Pyrosphere
This section has been reserved for the care and feeding of animals that can survive in an artificial atmosphere of extreme heat." —Exam Center computer (Metroid: Other M)
- " Something was gnawing at me. Communication with Adam had ceased." —Samus Aran (Metroid: Other M)
- "It's a place like Tourian, where we propagate and raise Metroids." —MB (Metroid: Other M)
- "You know what lies up ahead: the Metroids and the artificial intelligence that controls them. The fruit of the Galactic Federation's twisted project." —Adam Malkovich (Metroid: Other M)
- "We developed an AI program that would reproduce Mother Brain's thought processes. We called it MB." —MB (Metroid: Other M)
- "...Sector Zero has a self-destruct protocol. If the sector receives a significant amount of damage, the unit is programmed to detach and self-destruct. A powerful explosion will eliminate the Metroids and MB without leaving a trace." —Adam Malkovich (Metroid: Other M)