The G.F.S. Aegis is a spaceship in the Federation Fleet, depicted in Metroid Prime: Federation Force. The ship serves as the Federation Force's resting stop in between missions and is commanded by General Alex Miles.
In M10: Black Hole, it is seen under threat of destruction from interstellar missiles in the possession of the Space Pirates. A Federation Marine team dispatched by the Galactic Federation barely managed to destroy the Transport ships carrying these missiles before the Aegis could be destroyed. The Aegis also appears to be the location of a Blast Ball arena.
The word "aegis" refers to protection, which this ship receives when the Federation attacks the Pirates before they can destroy the Aegis ship.
"Pirates are attempting to bring down the Aegis with interstellar missiles."
"The Pirates have constructed interstellar missiles capable of destroying the Aegis. The missiles are being delivered via transport ship through a wormhole. It is imperative that you destroy those missiles before they can be delivered to the launcher."