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Not much is known about the Command Shuttle except that surviving Marines were brought there, according to Cortana in the level Halo. In early Halo canon, it would have presumably functioned as some form of operations base for the human forces. It was only mentioned once, and no official sources have referred to it since. With the release of Halo: The Flood, the concept of this command shuttle was replaced with Alpha Base.
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.
The Command Shuttle may have been an SKT-13 Shuttle, a larger verion of the Bumblebee Lifepod, used to transfer the survivors to the Firebase.