Destruction of Prime Base
How about this.
Prime Base is an active facility. The backup is a frozen facility.
The Project orders several tens of thousands of doses of Smallpox Vaccine in the Early 1980s. This would be odd, since the disease has been officially eradicated. Krell saw this as a sign that something was up and tainted a portion of the vaccine with a newly developed weaponized prion. He hoped that all of the Project would get the tainted lot but the luck of the draw saw it sent to Prime Base. It was stockpiled. During the war it became obvious that smallpox had been heavily weaponized by the Soviets and a large number of warheads with that agent were used against North America. As a wise precaution the entire Prime Base population was vaccinated against smallpox in the days after the war. This was a slow motion death sentence. It took three months before the first symptoms arose and another month before it was obvious that 100% of the population of a totally seal environment were all exhibiting similar symptoms. A month after that came the first fatalities. The Universal Antibody was completely useless against it, since it isn't an organism. The scientists at Prime did discover what it was and that it wasn't really infectious. If it had been they would have self destructed the base to prevent the spread of the disease. Their notes are available in the base.
There is no colony. There was no Krell Nuke and Krell has no idea where the base is. Prime did not send the recall signal to secondary base because they aren't certain if that lot of vaccine was also tainted. They did send all their data to the best medical base they had, which was to determine if a cure was possible and this base was given the wake up codes for Secondary base and several other teams. It was felt that even if this medical base had the tainted vaccine perhaps they could come up with a treatment before they began to suffer from the illness. They were not to wake up any additional teams unless they had the cure, since Prime Base thought all the lots had been tainted. This explains why no external wakes ups were ever sent. It was believed that once a team awoke it would have a maximum life expectancy of six months or less.
Krell did find the Medical base and did destroy them before they could get much traction. They were able to self-destruct the recall data and everything else Krell wanted before they were overrun.
In Prime Base they didn't do the "Final Deception" because there was no need. They did do the "Grand Deception" in the off chance someone besides MP showed up first. They told the Medical base all about it, so they would walk right through the disguise.
The disease causes paranoia, aggression loss of motor control and lots of other things typical of these ailments and made the last few weeks in Prime Hell as people went mad. The mass suicide was not to make the end easier for the people; it was to keep them from destroying parts of the base accidently in their dementia.
So this explains:
How the base was knocked out
Why EVERYONE died
Why the mass suicide
Why the Grand Deception
Why Secondary Base never woke up
Why the teams were never recalled
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