NOTE: Very Spinfoil
So the darkness is on the moon, There is no denying that, but how did it get there and how did we not see it? Well I have a theory. You see, Back in D1 there was a crucible map by the name of “Anomaly”, This crucible map was what appeared to be a smaller golden age moon base in Mare Cognitum. However, what made this crucible map stand out was the massive, enclosed object in the center of the map. You couldn’t open it, it didn’t move, and it was pretty clear from how it was described that it’s meant to hold or contain something.
“[u.1:01] A Titan once tried to punch the Anomaly until it opened.” -Ghost Fragment: The Anomaly
But, besides being very strong, and “the casing is constructed in a manner that defies modern techniques.“, whatever that means. The anomaly has one last, very interesting property. It causes nightmares.
“Reports suggest that those who spent time in proximity to the Anomaly reported symptoms of insomnia, some so severe they required hospitalization. It was the City’s recommendation that only remote sensing equipment be used until such time that a full review of the existing data could be completed.”
-Ghost Fragment: The Anomaly
Insomnia’s main symptom, and its most notable one, is a loss of sleep. However that doesn’t mean that it doesn’t have other side-effects, one of which being “waking nightmares”, which is where a person experiences a nightmare more vividly and while awake due to lack of sleep. So we have an object that has weird, anomalous properties that causes nightmares and just so happens to reside in the exact place that the darkness randomly appears in, Mare Cognitum.
Do I think this is the official explanation? Probably not. But I did have a lot of fun researching this!