The Main Deck is the central area of the Biologic Space Laboratories research station. From the Main Deck, Samus can access the six sectors as well as the Habitation Deck, Operations Deck, Reactor Silo, and Docking Bay. It is also where Ridley's clone from Metroid: Other M is frozen in the Sub-Zero Containment room to be preserved.
- 3 Energy Tanks
- 7 Missile Tanks
- 3 Power Bomb Tanks
- Missile Launcher
- Morph Ball
- Space Jump
- Ice Beam
- Unnamed Suit
- Core-X (Arachnus/Neo-Ridley/SA-X)
- Dachora (Habitation Deck, non-hostile)
- Etecoon (Habitation Deck, non-hostile)
- Neo-Ridley (X Parasite escapes Ridley corpse)
- Omega Metroid
- Ridley (frozen in Sub-Zero Containment)
- X Parasite
- Zeta Metroid (shell left by Omega Metroid)
- Zombie researcher
"This area contains elevator access, storage, etc."
- The music theme that plays in this area is almost always different every time Samus visits it. On many occasions, Facing a Huge Reaction is heard. When Samus first enters the Main Deck, Environment Sound (Tension) is heard. In some cases, usually to foreshadow a bad event that will occur, the BGM will not play at all.