The Operations Deck is a collection of rooms that includes a Recharge Station, Save Station, Navigation Room, Data Room, and the Operations Room. The main room of the Operations Deck is where Samus finally confronts one of the SA-X. It is also the first area where Samus uses a Data Room to download Missile data, increasing her chances of survival from 10% to 20% according to Adam. This area also provided an alternate route to Arachnus through a ventilation shaft, which could be accessed through a grate vulnerable to Missiles, after the elevators were taken offline due to electrical interference. This ventilation shaft becomes blocked off when Samus returns to the Operations Deck to reach the Operations Room during her Final Mission aboard the B.S.L.
The Fusion website features an "Operations Deck" section, that serves as a recap of the plots of previous Metroid games.
- SA-X (near the end of the game, after receiving order from Adam to initiate the self-destruct sequence.)
- The bottom-left platform between the doorways leading to the Navigation Room and Save Room was originally more open spaced in the Prototype. Consequently, this change also affected the SA-X fight.
- The Ventilation Shaft that Samus uses to reach Arachnus becomes blocked off when she faces the SA-X. How it became destroyed remains unclear. It is likely the SA-X blocked it off in an attempt to stop Samus from reaching the Operations Room before she arrived. Given the explosion sound made upon reaching the door to the Operations Room, the SA-X possibly entered through the blocked off shaft as well. Furthermore, the SA-X's Core X escapes through the same blocked off shaft.