I imagine some kind of global entity, that have always been there, but about which little is known... From its origin, to its goals... Just there, surrounding everything.

I like it, seems so mysterious...

Yeah I think it has a lot of potential for multiple, very distinct, backstories. It's not the purpose here, but we can model any sort of alignment (good, bad, neutral, selfish, altruist, ...).

Even in terms of gameplay we can imagine more than simple spying. It would be great if it has the ability to influance the actions of another faction (AI or human). Maybe it's out of scope, but what about the possibility to send fake quest to other factions, that can provide an advantage to this spying faction, with a counterpart for the other (as a quest reward coming from them: dust, resources, tech, ...). This way, the "Presence" would always play in the backstage, manipulating others to reach their goals.

Oooooooooh Me likey