The Galactic Federation mothership is a Galactic Federation-operated spaceship seen at the beginning of Metroid: Other M. It features a quarantine room, empty training room and meeting room. While these locations are not revealed as part of a mothership in the game, its status was confirmed in issue 59 of Official Nintendo Magazine on page 76. 
Samus Aran is seen being rehabilitated in the quarantine room after her ordeal on Zebes. She awakens to the voice of the Head Quarantine Officer and enters the training room to test her skills at the officer's direction. After this is done, Samus enters the meeting room to report the destruction of the Metroids, and Zebes. The meeting room is guarded by a Retinal 10 Scan. After this, she departs the mothership. Unbeknownst to her, fragments of the baby were removed from her Varia Suit during her surgery, and then used by the ringleaders aboard the BOTTLE SHIP to clone Metroids.
- ^ Official Nintendo Magazine, issue 59, page 76 (September 2010): "As has been widely publicised, the story picks up directly after Super Metroid's climactic Mother Brain showdown (which is gloriously revisited in full high resolution technicolour in the first of many magnificent cutscenes). Samus awakens on a Galactic Federation mothership, successfully patched up after the gruelling battle. Following a brief tutorial section where you have the chance to get to grips with the game's new control set-up in a training area, she jumps into her ship and sets off to investigate a distress call broadcast from a mysterious space station known as The Bottle Ship stranded in the depths of space."