Samus first arrives after her investigation of Sector 1, and becomes cautious after she sees that a door has been broken open. Samus continues on into the control tower to find James Pierce, who arrived before everyone else, and is seemingly doing something under a computer. The rest of the 07th Platoon then appear, except for Lyle, whom the others assume is late. Maurice Favreau examines the computer which had "self-destructed", and will need time to repair it. Anthony Higgs suggests scouting the building, but not before reminding Samus the background of the Test Area; Federation Training Grounds.
As Samus explores the building, she stumbles upon a five-way access, and in the middle of the five, she finds the body of a cybernetically enhanced Zebesian, making strange beeping noises, which cease as it falls to the floor. Samus examines it and is shocked to discover a Galactic Federation insignia on the creature. At this point Maurice calls everyone back to the control tower, where he reads from a file he recovered that the BOTTLE SHIP is a breeding ground for creatures to be used as Bioweapons. Surprised by the idea of bioweapons being produced here, Samus says that Bioweapons were strictly illegal, and contemplates how this would go against Adam's philosophy and realizes that her bringing back the Infant Metroid from SR388 would also have done so.
Samus continues on and finds a room similar to where she encountered the Zebesian body, only to encounter a group of living ones hiding in the rafters instead. Anthony and the others come to her aid, but Adam orders everyone to evacuate the building while Samus deals with the threat. Samus defeats most of the Pirates, but two of the Zebesians run from the battle and hide in corridors, forcing Samus to track and destroy them.After defeating the Zebesians, Samus returns to the empty control tower to hear shouting and gunshots outside. Looking through the window, Samus sees the 07th Platoon battling a large purple lizard, which is glancing-off bullets. The creature spots Samus in the tower, whom rushing to the platoon's aid. Samus enters the grounds to see Anthony pointing behind her, shouting "Behind you!" (in slow motion), where the creature was hiding. Samus turns around too late, and the creature launches its trap; pinning Samus down and screaming. Suddenly, a swarm of Reos and Griptians appear, distracting the other soldiers, and forcing Samus to fend the creature off herself. Just when the creature is about to land a finishing blow on Samus, the creature is launched off her by a Plasma shot from Anthony, and it quickly escapes by slamming through an unseen wall hidden by the simulated environment. After the battle, they locate Lyle's body, which is torn to shreds. Adam requests that Samus follow the creature.
When Samus heads to the Pyrosphere via a nearby access, the Exam Center explodes.
- There is an odd occurrence in the room containing vending machines. The machines display what appears to be food alongside other cases, one of which has the name "Ghalmanian" displayed on it. Ghalmanians are purple chameleon-like creatures Samus encountered earlier in the Biosphere. What these cases are or what they contain remains unclear, along with their purpose. Several can be found on the floor amongst other cases and glass from a broken vending machine.
- The packages of food resemble what would be sold in Japanese vending machines, this is obviously because Other M was developed in Japan. The packages are difficult to make out, but two of them are blue and yellow with some sort of "C" or bracket-like symbol. Another package is white with light green circles and a blue box, possibly green grapes, apples or pears. Another package features what may be either potatoes, mushrooms or white cheese. A final package has what may be a cat on it.
- Several destroyed FG II-Graham robots with their wings folded in can be found on the floors of some of the rooms in the Center. It is likely that they were disengaged by James prior to Samus' arrival.
- How the Exam Center blew up remains a mystery. When the Deleter, James Pierce, arrives at the Exam Center first, he may have been putting explosives under the computer. Also, in the second encounter with MB (who posed as Madeline Bergman), Samus theorizes that she destroyed the Exam Center as an act to eliminate all the data confined there.
|Areas of the BOTTLE SHIP|
|Areas||Main Sector • Sector 1 / Biosphere • Sector 2 / Cryosphere • Sector 3 / Pyrosphere|
|Sub-Areas||Bioweapon Research Center • Experimental simulated desert area • Section 4 Gravity Block • Sector Zero|
|Rooms|| Main Sector: Spaceport • Bottle Ship Control Room • Bottle Ship Residential Area • Cargo Hold • Control Bridge • Main Elevator |
System Management room
Biosphere: Biological Experiment Floor • Experiment Floor 3 • Biosphere Test Area • Breeding Room • Exam Center
Observation Room • Scrap Block • Subterranean Control Room
Cryosphere: Experiment Floor • Materials Storehouse • Materials Transfer Lift • Water Tank • Nightmare's Room
Sector Generator Room
Pyrosphere: Blast Furnace Observation • Crater Interior • Desert Refinery • Environmental Test Floor
Floor Observation Room • Geothermal Power Plant
Bioweapon Research Center: Room MW