Command shuttle

Not much is known about the Command Shuttle except that surviving Marines were brought there, according to Cortana in the level Halo.

Speculation
This could be where Keyes was transmitting his message to the Master Chief during the level The Silent Cartographer. He couldn't have been on the Pillar of Autumn because it had crashed. However, he could have been on a Pelican Dropship, or it may refer to Alpha Base.