The Desert Refinery is a large room where sand in the surrounding desert area is refined. Whether this serves a purpose for the bioweapons projects aboard the BOTTLE SHIP, or is for general maintenance is unknown. Several towers in the room are seen grinding and releasing sand particles.
Samus ascends eight flights of stairs to progress through this room, encountering numerous enemies. She is not required to kill the enemies to proceed, but doing so assists with navigation as they are removed as obstacles. Before each flight of stairs is a square or rectangular platform lined with railing. There are Heat Bulls on the first three flights of stairs, and on the fourth platform up, Samus begins to encounter Super Zebesians.
On the top floor, the path turns onto a diagonal walkway leading to a wall. Samus can get to the top of it using a Grapple Point. The wall turns into another path leading toward a large, spinning turbine with several ledges surrounding it that Samus can grab. By Kick Climbing off the left wall to the ledges, Samus can slowly climb the turbine to a higher platform. Alternatively, she can quickly Kick Climb from the right side of the turbine and the wall underneath the platform to reach the top. A similar puzzle appears in the Sector Generator Room in Sector 2.
Continuing on, Samus will come to another turbine that she can climb in the same manner. Sovas are found on the walls Samus uses to jump off onto the turbines.
Climbing the second turbine will bring her to another walkway, with a terminal to unlock the exit door. Samus can reach that by climbing to the top of the first turbine and jumping to the platform on the right. Through the next corridor, Samus enters a ventilation shaft in Morph Ball form above the Desert Refinery. The shaft splits into two paths: the right path leads to a Missile Tank, while the left path leads to an upper ledge with the Navigation Booth. From there, Samus continues on to the "Sand Tower summit", where she battles the Rhedogian again.
- "Mella stairwell" (via automatic door)
- "Curving catwalk" (via automatic door)
- Navigation Booth F (via automatic door)
- Missile Tank
- In the Morph Ball tunnel at the top of the room, there is a branching path. The Tank at the end of the path that leads right.