The Main Sector is the central hub of the Bottle Ship and is the largest sector Samus Aran explores during her mission there. A portion of it composes the Landing Site of both Samus's Gunship and the Galactic Federation ship belonging to the Galactic Federation 07th Platoon. When first explored, it is relatively devoid of enemies, and its power supply is non-operational. Initially, exploration of the sector is mainly limited to the Control Room and the Main Elevator. The Control Room is where Samus and the 07th Platoon encounter the Brug Mass and receive their orders, given by Adam Malkovich, who also authorizes many of Samus's weapons from here, with the Missiles and Bombs being the first. The Main Elevator is a large, almost cylindrical machine located near the rear of the sector that provides access to the Bottle Ship's three simulated-environment sectors: Sector 1, the Biosphere, Sector 2, the Cryosphere, and Sector 3, the Pyrosphere. After power is restored via a terminal in the System Management Room, Samus is able to reach previously inaccessible areas via other terminals and minor elevators, and the sector becomes infested with enemies.
Much of the sector remains inaccessible until Samus obtains Power Bombs, as they are required to activate the Desbrachians that block several doors throughout the sector and the Bottle Ship as a whole. Using them, Samus gains access to two of the sector's most important rooms: the Residential Quarters and the Control Bridge. The Residential Quarters presumably housed Madeline Bergman and her staff before the former sent out the distress signal that brought Samus and the 07th Platoon to the Bottle Ship, as the quarters are empty when Samus explores them, though initial exploration is entrusted to K.G. Misawa. The Control Bridge, left to the jurisdiction of James Pierce, contains the Bottle Ship's navigational equipment and is where Samus encounters Phantoon.
- "And Samus, I'm authorizing missile use." —Adam Malkovich (Metroid: Other M)
- "Regarding auxiliary weapons, the use of bombs has been authorized. As far as your other weapons go, we will continue to investigate and authorize use as we can." —Adam Malkovich (Metroid: Other M)
- "And Samus. You go to the System Management Room. Do everything you can to get the electrical system back up and running." —Adam Malkovich (Metroid: Other M)
- "And K.G.! Run a complete sweep of the residential quarters and investigate for any trace of survivors." —Adam Malkovich (Metroid: Other M)
- "James! Check out the Control Bridge. Our communication issues might be the result of electrical interference." —Adam Malkovich (Metroid: Other M)