Eventually, Wheatley is defeated by the duo and GLaDOS manages to have the previously hidden Core Transfer Hatch plug her back into her body. It also appears Wheatley has decided to raise the room closer to the surface. Since the last visit, Chell has inadvertently sent pumps of Mobility Gels up into the new facility, which she witnesses are being pumped under the room, along with bombs. The chamber is witnessed again at the end of the game upon Chell and GLaDOS' return to the upper structure and completion of several tests composed by Wheatley.

The power almost immediately takes over Wheatley, prompting him to transfer GLaDOS' core into a potato battery and plunge both her and Chell into the depths of the facility. Via Core Transfer, GLaDOS' core is removed from her body and replaced with Wheatley's, giving him control of the facility. Despite this, it appears protocol has forced GLaDOS to retain specific elements of the chamber as part of design, including a Core Transfer Hatch and a Stalemate Resolution Annex. When Chell returns by Wheatley's assistance to the room at the midpoint of the game, the room has been completely reconstructed in a form bearing little resemblance to the original chamber created by Aperture staff.

Portal 2 incinerator room