So we know that whoever has control of the MPD has control of the zombies. The timeline says, “Facing defeat, the Corrupted Keepers hide the Aether Pyramid on a moon within one of the newly discovered dimensions.” From this we see that there is only ONE of these pyramids in the entirety of zombies, just like how there is only one Summoning Key. So now we know that the Aether Pyramid (the MPD) is a device that allows absolute power (control over the zombies). They desire, above all else, to return to Agartha.”
Trapped in the Dark Aether, The Corrupted Keepers contort and evolve over Eons, ultimately becoming the Apothicons. After banishing the Corrupted Keepers to the Dark Aether beneath creation, the remaining Keepers take on the mantle of Guardians. “The War of Agartha Ends: Facing defeat, the Corrupted Keepers hide the Aether Pyramid on a moon within one of the newly discovered dimensions. A schism forms between them and the Keepers untainted by the Dark Aether.” “The Aether Pyramid: The corrupted Keepers create the Aether Pyramid, a device capable of absolute power. I was reading through the timeline today and came across a couple excerpts that provide some insight on how the eyes work: But in Shadows of Evil, Zetsubou No Shima, Gorod Krovi, and Revelations, we definitely know that Samantha never went in the MPD. We know that The Giant and Der Eisendrache take place in the same dimension as the beginning dimension (but became a fracture), but we do not know why Samantha never entered the pyramid (perhaps this will be answered in the next game). Origins and Black Ops 3 caused some confusion as to what the eye color meant because in these maps, Samantha supposedly never entered the MPD. This only applies for the beginning dimension though. In Buried, the eyes switch to orange when completing the Maxis side of the easter egg. In Moon and Nuketown Zombies, the eyes switch from yellow to blue when Richtofen switches bodies with Samantha.
This is proved in Black Ops 1 and Black Ops 2. In the beginning dimension, what we know for a fact is that yellow eyes means Samantha is controlling them, blue eyes means Richtofen is controlling them, and orange eyes means Maxis is controlling them. There is an excerpt from the timeline which may help with discovering how the zombie's eye color works.