After Adam restored power to the Main Elevator, he ordered Samus to investigate the Habitation Deck for chances of survivors. The worm creature Fune (and later Namihe) inhabited much of the area. Samus did not find any humans in the main Habitation Deck, much to Adam's dismay. However, she did find her old friends, the Dachoras and Etecoons, in their first chronological appearance since the destruction of planet Zebes in Super Metroid. They were found behind a glass window, with the Dachoras running around and the Etecoons hanging off tire swings. The terminal to open their containment was blocked by a Shutter, so Samus entered the room from the other side via a secret chamber. She opened the chamber and found to her surprise the Dachoras and Etecoons running out of the room, to her Gunship.
- A Missile Tank is contained in the Habitation Deck's bottom section.
- The Habitation Deck may have been the living quarters of the researchers inside the station, similar to the BOTTLE SHIP's Residential Sector.
- The theme heard in this area is "Facing a Huge Reaction", named so in the tracklist for the Metroid Prime & Fusion Original Soundtracks.