We know the APD existed in the original timeline, as it's mentioned in the comics. And in Alpha Omega, we learn it has the power to control the zombies.. now whether that's the APD in affect, or Cornelius Pernell, is irrelevant. But why wasn't it used to contain the outbreak?
Couldn't they have posted up a few hundred APDs across the U.S. and called it a day? And if it truly is the host controlling them from inside, then I guess you could argue the Aether, or Agartha.. or whatever the APD is connected to, would've corrupted anyone in Pernell's position.
Per tradition, are Broken Arrow stupid?
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In the original timeline, there isn’t really an outbreak until Moon. Not to also mention that in the events of Nuketown zombies, the facility is overrun by zombies. Furthermore, we can assume with the dropping of the missiles on the earth, in which Nuketown is hit, that the bunker containing the APD was heavily impacted to the point where it was forgotten.
Also worth noting that Broken Arrow may not have known what the actual purpose of either Pyramid was