The room is square in shape and has two floors; Samus enters from the bottom floor the first time. Another hatch, which is locked on the first visit, leads to another room that Samus can explore when she returns to the BOTTLE SHIP. The second floor contains an elevator that is used in a cutscene, but cannot be used in gameplay. On the first visit, the second floor's walls are lined with dormant Desbrachian pods. There is no access between the two floors in the control room itself, so Samus will have to backtrack if she falls to the bottom floor. Concept art of the Bioweapon Research Center suggests that this room is for observation of the Queen Metroid, in the nearby Room MW.
After encountering a survivor of the BOTTLE SHIP in Room MW, Samus destroys a Queen Metroid that the survivor releases in an attempt to kill Samus, who she assumes is an assassin sent to silence her. The survivor's hiding chamber is breached by the Power Bomb Samus uses to destroy the Queen, and she quickly flees. Samus pursues her to this room and corners her against a door. Fearing for her life, the survivor screams at Samus to not come any closer. Samus calmly introduces herself and explains that she is here to rescue the woman. She asks if she may approach her, and the survivor acquiesces.
The survivor introduces herself as Madeline Bergman, the director of the illegal bioweapons project on the BOTTLE SHIP. Confused, Samus explains that she met another female survivor who identified herself as such. Madeline shows her ID badge and clarifies that the woman Samus met before was MB in android form. Madeline proceeds to explain the truth behind MB's rampage and her relationship with "Melissa", as she called the android. While Samus listens, she pieces together the events that transpired before her arrival through a monologue.
As Madeline states that MB has been backed into a corner, with her plans to attack the Galactic Federation foiled, the girl appears, brandishing a Freeze Gun. A standoff between Samus and MB ensues; Samus attempts to shield Madeline, but she steps out from behind the Bounty Hunter and attempts to apologize to the android. She seems to succeed, as MB lowers her weapon. However, she apparently senses an incoming Freeze Gun blast, and pushes Madeline out of its path. The blast freezes over Melissa.
The Federation Army storms the control room and surrounds MB, Madeline and Samus, ordering them not to move. Seconds later, MB thaws and throws her Freeze Gun towards Madeline, before telepathically summoning hordes of Desbrachians, Ghalmanians and Mighty Griptians to attack the soldiers. Samus orders Madeline to stay behind her, acting as her human shield. In the ensuing battle, Samus uses her Missiles to continually blast Desbrachians out of her line of sight, until she has a clear shot at MB. Upon using Examine on MB, another cutscene ensues.
Madeline picks up the Freeze Gun, and reluctantly fires at MB, re-freezing her. The Colonel that was leading the soldiers orders a number of snipers concealed on the second floor to fire at MB, killing her. The Desbrachians disintegrate around a sobbing Madeline, who collapses in front of her fallen "daughter". The Colonel descends to the lower floor via the elevator, and steps on MB's hairclip, which had fallen off of her head when she pushed Madeline. His men hold Samus at gunpoint. The Colonel approaches Samus, thanking her for her service while reminding her that as she is an independent Bounty Hunter, and all members of the 07th Platoon she was working with are dead, she is barred from any contact with Madeline. He admonishes her for her "predilection for transporting electric cargo, like infant Metroids", referring to the baby, and orders a soldier to escort her to her Gunship.
A soldier takes her by the arm and says "Time for us to go. C'mon, Princess." Confused, the Colonel demands the soldier's identity. He reveals himself as Anthony Higgs, the last surviving soldier in the 07th Platoon. Since he is still alive, his orders from Adam Malkovich (approved by the Chairman of the Galactic Federation) to secure the safety of any survivors override the Colonel's authority. Samus and Anthony smile at each other, before leaving the room with Madeline.
The control room can be accessed in gameplay upon Samus's return to the BOTTLE SHIP after the credits. The hairclip is no longer present, suggesting someone, likely Madeline took it. The door that Samus cornered her in front of can now be opened, and leads to another room full of computer monitors, with some expansions.
Gallery Mode notes
"The part between the 2F loft and the ceiling has a gloomy impression (as if snipers are concealed there). Design the room's size as 20m high x 30m long. Design the room's full height at 20m, and it is 10m to the loft scaffolding."
"For the setup of the room where the climax scene takes place, I think we should design it as the control room for observation of the Queen Metroid's breeding. Facing from the central door, the room's features include all sorts of monitors and control panels, and a lift installed on the right, giving the impression it's a little messy."