Was the Pyramid ship on the Moon before the Traveler even started coming to us?

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.

Quite possible, yes.

Well, the Traveler did fight the Darkness right above the Earth. Once the Darkness was defeated, the Traveler died and created the Ghosts. In doing so, the darkness no longer needed to be active, because the Traveler wasn’t. It’s like a Yin-Yang thing where if there is light, there has to be dark. So wherever the ships were when the Traveler was defeated is where they will be now.

One small thing, the Traveler didn’t die, it became more comatose then dead…

Just about to say this. It was definitely more sleeping than dead, because from my understanding Ghosts are just conduits fro the Light, a channel from the Traveler to the Guardian, and if it was dead it likely couldn’t revive Guardians or create new ones. Also, if it was dead it wouldn’t have been able to thermo-nuke Ghaul, but @XxDredgenXAKAIxX I do agree with the whole Yin-Yang deal because when the Traveler woke, the cutscene after showed the Pyramids waking up too so they are likely connected in that way.