From what I can tell, from reading the lore book Revelations. It seems that the ship was there for a long time. Since the miners were there before the collapse and during it we got to see what it was like on the moon. The nightmares have been on the moon along with the insomnia and all of the other symptoms of its present’s.
If I’m correct then this could mean there could be multiple Pyramids throughout the system in hiding from before the Travelers arrival.