Command shuttle

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. The command shuttle is the lifeboat that brought down all vital bridge crew from the Pillar of Autumn and landed them safely on 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. This theory has been disproved. During the time of the Assault on the Cartographer, Keyes was on Alpha Base, overseeing the assault. He also was readying for the attack on the "weapons cache" in the Swamp.

The Command Shuttle may have been an SKT-13 Shuttlecraft, a larger version of the Bumblebee Lifepod, used to transfer the survivors to the Firebase.

The Command Shuttle was overrun by Covenant forces shortly after it's uneventful landing. It is highly unlikely that any UNSC forces regrouped there; the position was comprimised.